# HG changeset patch # User iuc # Date 1623222042 0 # Node ID 60eec78ee26f4549008945da9ec28b706f573205 # Parent 5e8d0e777033511041c6e2645a454052102aeae3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97" diff -r 5e8d0e777033 -r 60eec78ee26f scripts/hyphy_summary.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/hyphy_summary.py Wed Jun 09 07:00:42 2021 +0000 @@ -0,0 +1,668 @@ +import argparse +import json +import re +from collections import defaultdict + +import BioExt +from Bio import SeqIO +from Bio.Seq import Seq +from Bio.SeqRecord import SeqRecord +from BioExt.uds import _align_par + + +class HyPhySummary(object): + + def __init__(self, arguments, summary_json=None, annotation_json=None): + self.arguments = arguments + self.ref_map = '' + self.summary_json = {} + self.annotation_json = {} + self.include_in_annotation = {} + self.test_map = {} + self.site_reports = {} + self.labels = {} + self.ref_seq_map = [] + self.cfel = {} + self.relax = {} + self.busted = {} + self.slac = {} + self.fel = {} + self.meme = {} + self.meme_full = {} + self.prime = {} + self.fade = {} + self.bgm = {} + self.ref_genes = [ + ['genome', 'ATTAAAGGTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAACGAACTTTAAAATCTGTGTGGCTGTCACTCGGCTGCATGCTTAGTGCACTCACGCAGTATAATTAATAACTAATTACTGTCGTTGACAGGACACGAGTAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCAGCACATCTAGGTTTCGTCCGGGTGTGACCGAAAGGTAAGATGGAGAGCCTTGTCCCTGGTTTCAACGAGAAAACACACGTCCAACTCAGTTTGCCTGTTTTACAGGTTCGCGACGTGCTCGTACGTGGCTTTGGAGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAGATGGCACTTGTGGCTTAGTAGAAGTTGAAAAAGGCGTTTTGCCTCAACTTGAACAGCCCTATGTGTTCATCAAACGTTCGGATGCTCGAACTGCACCTCATGGTCATGTTATGGTTGAGCTGGTAGCAGAACTCGAAGGCATTCAGTACGGTCGTAGTGGTGAGACACTTGGTGTCCTTGTCCCTCATGTGGGCGAAATACCAGTGGCTTACCGCAAGGTTCTTCTTCGTAAGAACGGTAATAAAGGAGCTGGTGGCCATAGTTACGGCGCCGATCTAAAGTCATTTGACTTAGGCGACGAGCTTGGCACTGATCCTTATGAAGATTTTCAAGAAAACTGGAACACTAAACATAGCAGTGGTGTTACCCGTGAACTCATGCGTGAGCTTAACGGAGGGGCATACACTCGCTATGTCGATAACAACTTCTGTGGCCCTGATGGCTACCCTCTTGAGTGCATTAAAGACCTTCTAGCACGTGCTGGTAAAGCTTCATGCACTTTGTCCGAACAACTGGACTTTATTGACACTAAGAGGGGTGTATACTGCTGCCGTGAACATGAGCATGAAATTGCTTGGTACACGGAACGTTCTGAAAAGAGCTATGAATTGCAGACACCTTTTGAAATTAAATTGGCAAAGAAATTTGACACCTTCAATGGGGAATGTCCAAATTTTGTATTTCCCTTAAATTCCATAATCAAGACTATTCAACCAAGGGTTGAAAAGAAAAAGCTTGATGGCTTTATGGGTAGAATTCGATCTGTCTATCCAGTTGCGTCACCAAATGAATGCAACCAAATGTGCCTTTCAACTCTCATGAAGTGTGATCATTGTGGTGAAACTTCATGGCAGACGGGCGATTTTGTTAAAGCCACTTGCGAATTTTGTGGCACTGAGAATTTGACTAAAGAAGGTGCCACTACTTGTGGTTACTTACCCCAAAATGCTGTTGTTAAAATTTATTGTCCAGCATGTCACAATTCAGAAGTAGGACCTGAGCATAGTCTTGCCGAATACCATAATGAATCTGGCTTGAAAACCATTCTTCGTAAGGGTGGTCGCACTATTGCCTTTGGAGGCTGTGTGTTCTCTTATGTTGGTTGCCATAACAAGTGTGCCTATTGGGTTCCACGTGCTAGCGCTAACATAGGTTGTAACCATACAGGTGTTGTTGGAGAAGGTTCCGAAGGTCTTAATGACAACCTTCTTGAAATACTCCAAAAAGAGAAAGTCAACATCAATATTGTTGGTGACTTTAAACTTAATGAAGAGATCGCCATTATTTTGGCATCTTTTTCTGCTTCCACAAGTGCTTTTGTGGAAACTGTGAAAGGTTTGGATTATAAAGCATTCAAACAAATTGTTGAATCCTGTGGTAATTTTAAAGTTACAAAAGGAAAAGCTAAAAAAGGTGCCTGGAATATTGGTGAACAGAAATCAATACTGAGTCCTCTTTATGCATTTGCATCAGAGGCTGCTCGTGTTGTACGATCAATTTTCTCCCGCACTCTTGAAACTGCTCAAAATTCTGTGCGTGTTTTACAGAAGGCCGCTATAACAATACTAGATGGAATTTCACAGTATTCACTGAGACTCATTGATGCTATGATGTTCACATCTGATTTGGCTACTAACAATCTAGTTGTAATGGCCTACATTACAGGTGGTGTTGTTCAGTTGACTTCGCAGTGGCTAACTAACATCTTTGGCACTGTTTATGAAAAACTCAAACCCGTCCTTGATTGGCTTGAAGAGAAGTTTAAGGAAGGTGTAGAGTTTCTTAGAGACGGTTGGGAAATTGTTAAATTTATCTCAACCTGTGCTTGTGAAATTGTCGGTGGACAAATTGTCACCTGTGCAAAGGAAATTAAGGAGAGTGTTCAGACATTCTTTAAGCTTGTAAATAAATTTTTGGCTTTGTGTGCTGACTCTATCATTATTGGTGGAGCTAAACTTAAAGCCTTGAATTTAGGTGAAACATTTGTCACGCACTCAAAGGGATTGTACAGAAAGTGTGTTAAATCCAGAGAAGAAACTGGCCTACTCATGCCTCTAAAAGCCCCAAAAGAAATTATCTTCTTAGAGGGAGAAACACTTCCCACAGAAGTGTTAACAGAGGAAGTTGTCTTGAAAACTGGTGATTTACAACCATTAGAACAACCTACTAGTGAAGCTGTTGAAGCTCCATTGGTTGGTACACCAGTTTGTATTAACGGGCTTATGTTGCTCGAAATCAAAGACACAGAAAAGTACTGTGCCCTTGCACCTAATATGATGGTAACAAACAATACCTTCACACTCAAAGGCGGTGCACCAACAAAGGTTACTTTTGGTGATGACACTGTGATAGAAGTGCAAGGTTACAAGAGTGTGAATATCACTTTTGAACTTGATGAAAGGATTGATAAAGTACTTAATGAGAAGTGCTCTGCCTATACAGTTGAACTCGGTACAGAAGTAAATGAGTTCGCCTGTGTTGTGGCAGATGCTGTCATAAAAACTTTGCAACCAGTATCTGAATTACTTACACCACTGGGCATTGATTTAGATGAGTGGAGTATGGCTACATACTACTTATTTGATGAGTCTGGTGAGTTTAAATTGGCTTCACATATGTATTGTTCTTTCTACCCTCCAGATGAGGATGAAGAAGAAGGTGATTGTGAAGAAGAAGAGTTTGAGCCATCAACTCAATATGAGTATGGTACTGAAGATGATTACCAAGGTAAACCTTTGGAATTTGGTGCCACTTCTGCTGCTCTTCAACCTGAAGAAGAGCAAGAAGAAGATTGGTTAGATGATGATAGTCAACAAACTGTTGGTCAACAAGACGGCAGTGAGGACAATCAGACAACTACTATTCAAACAATTGTTGAGGTTCAACCTCAATTAGAGATGGAACTTACACCAGTTGTTCAGACTATTGAAGTGAATAGTTTTAGTGGTTATTTAAAACTTACTGACAATGTATACATTAAAAATGCAGACATTGTGGAAGAAGCTAAAAAGGTAAAACCAACAGTGGTTGTTAATGCAGCCAATGTTTACCTTAAACATGGAGGAGGTGTTGCAGGAGCCTTAAATAAGGCTACTAACAATGCCATGCAAGTTGAATCTGATGATTACATAGCTACTAATGGACCACTTAAAGTGGGTGGTAGTTGTGTTTTAAGCGGACACAATCTTGCTAAACACTGTCTTCATGTTGTCGGCCCAAATGTTAACAAAGGTGAAGACATTCAACTTCTTAAGAGTGCTTATGAAAATTTTAATCAGCACGAAGTTCTACTTGCACCATTATTATCAGCTGGTATTTTTGGTGCTGACCCTATACATTCTTTAAGAGTTTGTGTAGATACTGTTCGCACAAATGTCTACTTAGCTGTCTTTGATAAAAATCTCTATGACAAACTTGTTTCAAGCTTTTTGGAAATGAAGAGTGAAAAGCAAGTTGAACAAAAGATCGCTGAGATTCCTAAAGAGGAAGTTAAGCCATTTATAACTGAAAGTAAACCTTCAGTTGAACAGAGAAAACAAGATGATAAGAAAATCAAAGCTTGTGTTGAAGAAGTTACAACAACTCTGGAAGAAACTAAGTTCCTCACAGAAAACTTGTTACTTTATATTGACATTAATGGCAATCTTCATCCAGATTCTGCCACTCTTGTTAGTGACATTGACATCACTTTCTTAAAGAAAGATGCTCCATATATAGTGGGTGATGTTGTTCAAGAGGGTGTTTTAACTGCTGTGGTTATACCTACTAAAAAGGCTGGTGGCACTACTGAAATGCTAGCGAAAGCTTTGAGAAAAGTGCCAACAGACAATTATATAACCACTTACCCGGGTCAGGGTTTAAATGGTTACACTGTAGAGGAGGCAAAGACAGTGCTTAAAAAGTGTAAAAGTGCCTTTTACATTCTACCATCTATTATCTCTAATGAGAAGCAAGAAATTCTTGGAACTGTTTCTTGGAATTTGCGAGAAATGCTTGCACATGCAGAAGAAACACGCAAATTAATGCCTGTCTGTGTGGAAACTAAAGCCATAGTTTCAACTATACAGCGTAAATATAAGGGTATTAAAATACAAGAGGGTGTGGTTGATTATGGTGCTAGATTTTACTTTTACACCAGTAAAACAACTGTAGCGTCACTTATCAACACACTTAACGATCTAAATGAAACTCTTGTTACAATGCCACTTGGCTATGTAACACATGGCTTAAATTTGGAAGAAGCTGCTCGGTATATGAGATCTCTCAAAGTGCCAGCTACAGTTTCTGTTTCTTCACCTGATGCTGTTACAGCGTATAATGGTTATCTTACTTCTTCTTCTAAAACACCTGAAGAACATTTTATTGAAACCATCTCACTTGCTGGTTCCTATAAAGATTGGTCCTATTCTGGACAATCTACACAACTAGGTATAGAATTTCTTAAGAGAGGTGATAAAAGTGTATATTACACTAGTAATCCTACCACATTCCACCTAGATGGTGAAGTTATCACCTTTGACAATCTTAAGACACTTCTTTCTTTGAGAGAAGTGAGGACTATTAAGGTGTTTACAACAGTAGACAACATTAACCTCCACACGCAAGTTGTGGACATGTCAATGACATATGGACAACAGTTTGGTCCAACTTATTTGGATGGAGCTGATGTTACTAAAATAAAACCTCATAATTCACATGAAGGTAAAACATTTTATGTTTTACCTAATGATGACACTCTACGTGTTGAGGCTTTTGAGTACTACCACACAACTGATCCTAGTTTTCTGGGTAGGTACATGTCAGCATTAAATCACACTAAAAAGTGGAAATACCCACAAGTTAATGGTTTAACTTCTATTAAATGGGCAGATAACAACTGTTATCTTGCCACTGCATTGTTAACACTCCAACAAATAGAGTTGAAGTTTAATCCACCTGCTCTACAAGATGCTTATTACAGAGCAAGGGCTGGTGAAGCTGCTAACTTTTGTGCACTTATCTTAGCCTACTGTAATAAGACAGTAGGTGAGTTAGGTGATGTTAGAGAAACAATGAGTTACTTGTTTCAACATGCCAATTTAGATTCTTGCAAAAGAGTCTTGAACGTGGTGTGTAAAACTTGTGGACAACAGCAGACAACCCTTAAGGGTGTAGAAGCTGTTATGTACATGGGCACACTTTCTTATGAACAATTTAAGAAAGGTGTTCAGATACCTTGTACGTGTGGTAAACAAGCTACAAAATATCTAGTACAACAGGAGTCACCTTTTGTTATGATGTCAGCACCACCTGCTCAGTATGAACTTAAGCATGGTACATTTACTTGTGCTAGTGAGTACACTGGTAATTACCAGTGTGGTCACTATAAACATATAACTTCTAAAGAAACTTTGTATTGCATAGACGGTGCTTTACTTACAAAGTCCTCAGAATACAAAGGTCCTATTACGGATGTTTTCTACAAAGAAAACAGTTACACAACAACCATAAAACCAGTTACTTATAAATTGGATGGTGTTGTTTGTACAGAAATTGACCCTAAGTTGGACAATTATTATAAGAAAGACAATTCTTATTTCACAGAGCAACCAATTGATCTTGTACCAAACCAACCATATCCAAACGCAAGCTTCGATAATTTTAAGTTTGTATGTGATAATATCAAATTTGCTGATGATTTAAACCAGTTAACTGGTTATAAGAAACCTGCTTCAAGAGAGCTTAAAGTTACATTTTTCCCTGACTTAAATGGTGATGTGGTGGCTATTGATTATAAACACTACACACCCTCTTTTAAGAAAGGAGCTAAATTGTTACATAAACCTATTGTTTGGCATGTTAACAATGCAACTAATAAAGCCACGTATAAACCAAATACCTGGTGTATACGTTGTCTTTGGAGCACAAAACCAGTTGAAACATCAAATTCGTTTGATGTACTGAAGTCAGAGGACGCGCAGGGAATGGATAATCTTGCCTGCGAAGATCTAAAACCAGTCTCTGAAGAAGTAGTGGAAAATCCTACCATACAGAAAGACGTTCTTGAGTGTAATGTGAAAACTACCGAAGTTGTAGGAGACATTATACTTAAACCAGCAAATAATAGTTTAAAAATTACAGAAGAGGTTGGCCACACAGATCTAATGGCTGCTTATGTAGACAATTCTAGTCTTACTATTAAGAAACCTAATGAATTATCTAGAGTATTAGGTTTGAAAACCCTTGCTACTCATGGTTTAGCTGCTGTTAATAGTGTCCCTTGGGATACTATAGCTAATTATGCTAAGCCTTTTCTTAACAAAGTTGTTAGTACAACTACTAACATAGTTACACGGTGTTTAAACCGTGTTTGTACTAATTATATGCCTTATTTCTTTACTTTATTGCTACAATTGTGTACTTTTACTAGAAGTACAAATTCTAGAATTAAAGCATCTATGCCGACTACTATAGCAAAGAATACTGTTAAGAGTGTCGGTAAATTTTGTCTAGAGGCTTCATTTAATTATTTGAAGTCACCTAATTTTTCTAAACTGATAAATATTATAATTTGGTTTTTACTATTAAGTGTTTGCCTAGGTTCTTTAATCTACTCAACCGCTGCTTTAGGTGTTTTAATGTCTAATTTAGGCATGCCTTCTTACTGTACTGGTTACAGAGAAGGCTATTTGAACTCTACTAATGTCACTATTGCAACCTACTGTACTGGTTCTATACCTTGTAGTGTTTGTCTTAGTGGTTTAGATTCTTTAGACACCTATCCTTCTTTAGAAACTATACAAATTACCATTTCATCTTTTAAATGGGATTTAACTGCTTTTGGCTTAGTTGCAGAGTGGTTTTTGGCATATATTCTTTTCACTAGGTTTTTCTATGTACTTGGATTGGCTGCAATCATGCAATTGTTTTTCAGCTATTTTGCAGTACATTTTATTAGTAATTCTTGGCTTATGTGGTTAATAATTAATCTTGTACAAATGGCCCCGATTTCAGCTATGGTTAGAATGTACATCTTCTTTGCATCATTTTATTATGTATGGAAAAGTTATGTGCATGTTGTAGACGGTTGTAATTCATCAACTTGTATGATGTGTTACAAACGTAATAGAGCAACAAGAGTCGAATGTACAACTATTGTTAATGGTGTTAGAAGGTCCTTTTATGTCTATGCTAATGGAGGTAAAGGCTTTTGCAAACTACACAATTGGAATTGTGTTAATTGTGATACATTCTGTGCTGGTAGTACATTTATTAGTGATGAAGTTGCGAGAGACTTGTCACTACAGTTTAAAAGACCAATAAATCCTACTGACCAGTCTTCTTACATCGTTGATAGTGTTACAGTGAAGAATGGTTCCATCCATCTTTACTTTGATAAAGCTGGTCAAAAGACTTATGAAAGACATTCTCTCTCTCATTTTGTTAACTTAGACAACCTGAGAGCTAATAACACTAAAGGTTCATTGCCTATTAATGTTATAGTTTTTGATGGTAAATCAAAATGTGAAGAATCATCTGCAAAATCAGCGTCTGTTTACTACAGTCAGCTTATGTGTCAACCTATACTGTTACTAGATCAGGCATTAGTGTCTGATGTTGGTGATAGTGCGGAAGTTGCAGTTAAAATGTTTGATGCTTACGTTAATACGTTTTCATCAACTTTTAACGTACCAATGGAAAAACTCAAAACACTAGTTGCAACTGCAGAAGCTGAACTTGCAAAGAATGTGTCCTTAGACAATGTCTTATCTACTTTTATTTCAGCAGCTCGGCAAGGGTTTGTTGATTCAGATGTAGAAACTAAAGATGTTGTTGAATGTCTTAAATTGTCACATCAATCTGACATAGAAGTTACTGGCGATAGTTGTAATAACTATATGCTCACCTATAACAAAGTTGAAAACATGACACCCCGTGACCTTGGTGCTTGTATTGACTGTAGTGCGCGTCATATTAATGCGCAGGTAGCAAAAAGTCACAACATTGCTTTGATATGGAACGTTAAAGATTTCATGTCATTGTCTGAACAACTACGAAAACAAATACGTAGTGCTGCTAAAAAGAATAACTTACCTTTTAAGTTGACATGTGCAACTACTAGACAAGTTGTTAATGTTGTAACAACAAAGATAGCACTTAAGGGTGGTAAAATTGTTAATAATTGGTTGAAGCAGTTAATTAAAGTTACACTTGTGTTCCTTTTTGTTGCTGCTATTTTCTATTTAATAACACCTGTTCATGTCATGTCTAAACATACTGACTTTTCAAGTGAAATCATAGGATACAAGGCTATTGATGGTGGTGTCACTCGTGACATAGCATCTACAGATACTTGTTTTGCTAACAAACATGCTGATTTTGACACATGGTTTAGCCAGCGTGGTGGTAGTTATACTAATGACAAAGCTTGCCCATTGATTGCTGCAGTCATAACAAGAGAAGTGGGTTTTGTCGTGCCTGGTTTGCCTGGCACGATATTACGCACAACTAATGGTGACTTTTTGCATTTCTTACCTAGAGTTTTTAGTGCAGTTGGTAACATCTGTTACACACCATCAAAACTTATAGAGTACACTGACTTTGCAACATCAGCTTGTGTTTTGGCTGCTGAATGTACAATTTTTAAAGATGCTTCTGGTAAGCCAGTACCATATTGTTATGATACCAATGTACTAGAAGGTTCTGTTGCTTATGAAAGTTTACGCCCTGACACACGTTATGTGCTCATGGATGGCTCTATTATTCAATTTCCTAACACCTACCTTGAAGGTTCTGTTAGAGTGGTAACAACTTTTGATTCTGAGTACTGTAGGCACGGCACTTGTGAAAGATCAGAAGCTGGTGTTTGTGTATCTACTAGTGGTAGATGGGTACTTAACAATGATTATTACAGATCTTTACCAGGAGTTTTCTGTGGTGTAGATGCTGTAAATTTACTTACTAATATGTTTACACCACTAATTCAACCTATTGGTGCTTTGGACATATCAGCATCTATAGTAGCTGGTGGTATTGTAGCTATCGTAGTAACATGCCTTGCCTACTATTTTATGAGGTTTAGAAGAGCTTTTGGTGAATACAGTCATGTAGTTGCCTTTAATACTTTACTATTCCTTATGTCATTCACTGTACTCTGTTTAACACCAGTTTACTCATTCTTACCTGGTGTTTATTCTGTTATTTACTTGTACTTGACATTTTATCTTACTAATGATGTTTCTTTTTTAGCACATATTCAGTGGATGGTTATGTTCACACCTTTAGTACCTTTCTGGATAACAATTGCTTATATCATTTGTATTTCCACAAAGCATTTCTATTGGTTCTTTAGTAATTACCTAAAGAGACGTGTAGTCTTTAATGGTGTTTCCTTTAGTACTTTTGAAGAAGCTGCGCTGTGCACCTTTTTGTTAAATAAAGAAATGTATCTAAAGTTGCGTAGTGATGTGCTATTACCTCTTACGCAATATAATAGATACTTAGCTCTTTATAATAAGTACAAGTATTTTAGTGGAGCAATGGATACAACTAGCTACAGAGAAGCTGCTTGTTGTCATCTCGCAAAGGCTCTCAATGACTTCAGTAACTCAGGTTCTGATGTTCTTTACCAACCACCACAAACCTCTATCACCTCAGCTGTTTTGCAGAGTGGTTTTAGAAAAATGGCATTCCCATCTGGTAAAGTTGAGGGTTGTATGGTACAAGTAACTTGTGGTACAACTACACTTAACGGTCTTTGGCTTGATGACGTAGTTTACTGTCCAAGACATGTGATCTGCACCTCTGAAGACATGCTTAACCCTAATTATGAAGATTTACTCATTCGTAAGTCTAATCATAATTTCTTGGTACAGGCTGGTAATGTTCAACTCAGGGTTATTGGACATTCTATGCAAAATTGTGTACTTAAGCTTAAGGTTGATACAGCCAATCCTAAGACACCTAAGTATAAGTTTGTTCGCATTCAACCAGGACAGACTTTTTCAGTGTTAGCTTGTTACAATGGTTCACCATCTGGTGTTTACCAATGTGCTATGAGGCCCAATTTCACTATTAAGGGTTCATTCCTTAATGGTTCATGTGGTAGTGTTGGTTTTAACATAGATTATGACTGTGTCTCTTTTTGTTACATGCACCATATGGAATTACCAACTGGAGTTCATGCTGGCACAGACTTAGAAGGTAACTTTTATGGACCTTTTGTTGACAGGCAAACAGCACAAGCAGCTGGTACGGACACAACTATTACAGTTAATGTTTTAGCTTGGTTGTACGCTGCTGTTATAAATGGAGACAGGTGGTTTCTCAATCGATTTACCACAACTCTTAATGACTTTAACCTTGTGGCTATGAAGTACAATTATGAACCTCTAACACAAGACCATGTTGACATACTAGGACCTCTTTCTGCTCAAACTGGAATTGCCGTTTTAGATATGTGTGCTTCATTAAAAGAATTACTGCAAAATGGTATGAATGGACGTACCATATTGGGTAGTGCTTTATTAGAAGATGAATTTACACCTTTTGATGTTGTTAGACAATGCTCAGGTGTTACTTTCCAAAGTGCAGTGAAAAGAACAATCAAGGGTACACACCACTGGTTGTTACTCACAATTTTGACTTCACTTTTAGTTTTAGTCCAGAGTACTCAATGGTCTTTGTTCTTTTTTTTGTATGAAAATGCCTTTTTACCTTTTGCTATGGGTATTATTGCTATGTCTGCTTTTGCAATGATGTTTGTCAAACATAAGCATGCATTTCTCTGTTTGTTTTTGTTACCTTCTCTTGCCACTGTAGCTTATTTTAATATGGTCTATATGCCTGCTAGTTGGGTGATGCGTATTATGACATGGTTGGATATGGTTGATACTAGTTTGTCTGGTTTTAAGCTAAAAGACTGTGTTATGTATGCATCAGCTGTAGTGTTACTAATCCTTATGACAGCAAGAACTGTGTATGATGATGGTGCTAGGAGAGTGTGGACACTTATGAATGTCTTGACACTCGTTTATAAAGTTTATTATGGTAATGCTTTAGATCAAGCCATTTCCATGTGGGCTCTTATAATCTCTGTTACTTCTAACTACTCAGGTGTAGTTACAACTGTCATGTTTTTGGCCAGAGGTATTGTTTTTATGTGTGTTGAGTATTGCCCTATTTTCTTCATAACTGGTAATACACTTCAGTGTATAATGCTAGTTTATTGTTTCTTAGGCTATTTTTGTACTTGTTACTTTGGCCTCTTTTGTTTACTCAACCGCTACTTTAGACTGACTCTTGGTGTTTATGATTACTTAGTTTCTACACAGGAGTTTAGATATATGAATTCACAGGGACTACTCCCACCCAAGAATAGCATAGATGCCTTCAAACTCAACATTAAATTGTTGGGTGTTGGTGGCAAACCTTGTATCAAAGTAGCCACTGTACAGTCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAAGCTATAGCCTCAGAGTTTAGTTCCCTTCCATCATATGCAGCTTTTGCTACTGCTCAAGAAGCTTATGAGCAGGCTGTTGCTAATGGTGATTCTGAAGTTGTTCTTAAAAAGTTGAAGAAGTCTTTGAATGTGGCTAAATCTGAATTTGACCGTGATGCAGCCATGCAACGTAAGTTGGAAAAGATGGCTGATCAAGCTATGACCCAAATGTATAAACAGGCTAGATCTGAGGACAAGAGGGCAAAAGTTACTAGTGCTATGCAGACAATGCTTTTCACTATGCTTAGAAAGTTGGATAATGATGCACTCAACAACATTATCAACAATGCAAGAGATGGTTGTGTTCCCTTGAACATAATACCTCTTACAACAGCAGCCAAACTAATGGTTGTCATACCAGACTATAACACATATAAAAATACGTGTGATGGTACAACATTTACTTATGCATCAGCATTGTGGGAAATCCAACAGGTTGTAGATGCAGATAGTAAAATTGTTCAACTTAGTGAAATTAGTATGGACAATTCACCTAATTTAGCATGGCCTCTTATTGTAACAGCTTTAAGGGCCAATTCTGCTGTCAAATTACAGAATAATGAGCTTAGTCCTGTTGCACTACGACAGATGTCTTGTGCTGCCGGTACTACACAAACTGCTTGCACTGATGACAATGCGTTAGCTTACTACAACACAACAAAGGGAGGTAGGTTTGTACTTGCACTGTTATCCGATTTACAGGATTTGAAATGGGCTAGATTCCCTAAGAGTGATGGAACTGGTACTATCTATACAGAACTGGAACCACCTTGTAGGTTTGTTACAGACACACCTAAAGGTCCTAAAGTGAAGTATTTATACTTTATTAAAGGATTAAACAACCTAAATAGAGGTATGGTACTTGGTAGTTTAGCTGCCACAGTACGTCTACAAGCTGGTAATGCAACAGAAGTGCCTGCCAATTCAACTGTATTATCTTTCTGTGCTTTTGCTGTAGATGCTGCTAAAGCTTACAAAGATTATCTAGCTAGTGGGGGACAACCAATCACTAATTGTGTTAAGATGTTGTGTACACACACTGGTACTGGTCAGGCAATAACAGTTACACCGGAAGCCAATATGGATCAAGAATCCTTTGGTGGTGCATCGTGTTGTCTGTACTGCCGTTGCCACATAGATCATCCAAATCCTAAAGGATTTTGTGACTTAAAAGGTAAGTATGTACAAATACCTACAACTTGTGCTAATGACCCTGTGGGTTTTACACTTAAAAACACAGTCTGTACCGTCTGCGGTATGTGGAAAGGTTATGGCTGTAGTTGTGATCAACTCCGCGAACCCATGCTTCAGTCAGCTGATGCACAATCGTTTTTAAACGGGTTTGCGGTGTAAGTGCAGCCCGTCTTACACCGTGCGGCACAGGCACTAGTACTGATGTCGTATACAGGGCTTTTGACATCTACAATGATAAAGTAGCTGGTTTTGCTAAATTCCTAAAAACTAATTGTTGTCGCTTCCAAGAAAAGGACGAAGATGACAATTTAATTGATTCTTACTTTGTAGTTAAGAGACACACTTTCTCTAACTACCAACATGAAGAAACAATTTATAATTTACTTAAGGATTGTCCAGCTGTTGCTAAACATGACTTCTTTAAGTTTAGAATAGACGGTGACATGGTACCACATATATCACGTCAACGTCTTACTAAATACACAATGGCAGACCTCGTCTATGCTTTAAGGCATTTTGATGAAGGTAATTGTGACACATTAAAAGAAATACTTGTCACATACAATTGTTGTGATGATGATTATTTCAATAAAAAGGACTGGTATGATTTTGTAGAAAACCCAGATATATTACGCGTATACGCCAACTTAGGTGAACGTGTACGCCAAGCTTTGTTAAAAACAGTACAATTCTGTGATGCCATGCGAAATGCTGGTATTGTTGGTGTACTGACATTAGATAATCAAGATCTCAATGGTAACTGGTATGATTTCGGTGATTTCATACAAACCACGCCAGGTAGTGGAGTTCCTGTTGTAGATTCTTATTATTCATTGTTAATGCCTATATTAACCTTGACCAGGGCTTTAACTGCAGAGTCACATGTTGACACTGACTTAACAAAGCCTTACATTAAGTGGGATTTGTTAAAATATGACTTCACGGAAGAGAGGTTAAAACTCTTTGACCGTTATTTTAAATATTGGGATCAGACATACCACCCAAATTGTGTTAACTGTTTGGATGACAGATGCATTCTGCATTGTGCAAACTTTAATGTTTTATTCTCTACAGTGTTCCCACCTACAAGTTTTGGACCACTAGTGAGAAAAATATTTGTTGATGGTGTTCCATTTGTAGTTTCAACTGGATACCACTTCAGAGAGCTAGGTGTTGTACATAATCAGGATGTAAACTTACATAGCTCTAGACTTAGTTTTAAGGAATTACTTGTGTATGCTGCTGACCCTGCTATGCACGCTGCTTCTGGTAATCTATTACTAGATAAACGCACTACGTGCTTTTCAGTAGCTGCACTTACTAACAATGTTGCTTTTCAAACTGTCAAACCCGGTAATTTTAACAAAGACTTCTATGACTTTGCTGTGTCTAAGGGTTTCTTTAAGGAAGGAAGTTCTGTTGAATTAAAACACTTCTTCTTTGCTCAGGATGGTAATGCTGCTATCAGCGATTATGACTACTATCGTTATAATCTACCAACAATGTGTGATATCAGACAACTACTATTTGTAGTTGAAGTTGTTGATAAGTACTTTGATTGTTACGATGGTGGCTGTATTAATGCTAACCAAGTCATCGTCAACAACCTAGACAAATCAGCTGGTTTTCCATTTAATAAATGGGGTAAGGCTAGACTTTATTATGATTCAATGAGTTATGAGGATCAAGATGCACTTTTCGCATATACAAAACGTAATGTCATCCCTACTATAACTCAAATGAATCTTAAGTATGCCATTAGTGCAAAGAATAGAGCTCGCACCGTAGCTGGTGTCTCTATCTGTAGTACTATGACCAATAGACAGTTTCATCAAAAATTATTGAAATCAATAGCCGCCACTAGAGGAGCTACTGTAGTAATTGGAACAAGCAAATTCTATGGTGGTTGGCACAACATGTTAAAAACTGTTTATAGTGATGTAGAAAACCCTCACCTTATGGGTTGGGATTATCCTAAATGTGATAGAGCCATGCCTAACATGCTTAGAATTATGGCCTCACTTGTTCTTGCTCGCAAACATACAACGTGTTGTAGCTTGTCACACCGTTTCTATAGATTAGCTAATGAGTGTGCTCAAGTATTGAGTGAAATGGTCATGTGTGGCGGTTCACTATATGTTAAACCAGGTGGAACCTCATCAGGAGATGCCACAACTGCTTATGCTAATAGTGTTTTTAACATTTGTCAAGCTGTCACGGCCAATGTTAATGCACTTTTATCTACTGATGGTAACAAAATTGCCGATAAGTATGTCCGCAATTTACAACACAGACTTTATGAGTGTCTCTATAGAAATAGAGATGTTGACACAGACTTTGTGAATGAGTTTTACGCATATTTGCGTAAACATTTCTCAATGATGATACTCTCTGACGATGCTGTTGTGTGTTTCAATAGCACTTATGCATCTCAAGGTCTAGTGGCTAGCATAAAGAACTTTAAGTCAGTTCTTTATTATCAAAACAATGTTTTTATGTCTGAAGCAAAATGTTGGACTGAGACTGACCTTACTAAAGGACCTCATGAATTTTGCTCTCAACATACAATGCTAGTTAAACAGGGTGATGATTATGTGTACCTTCCTTACCCAGATCCATCAAGAATCCTAGGGGCCGGCTGTTTTGTAGATGATATCGTAAAAACAGATGGTACACTTATGATTGAACGGTTCGTGTCTTTAGCTATAGATGCTTACCCACTTACTAAACATCCTAATCAGGAGTATGCTGATGTCTTTCATTTGTACTTACAATACATAAGAAAGCTACATGATGAGTTAACAGGACACATGTTAGACATGTATTCTGTTATGCTTACTAATGATAACACTTCAAGGTATTGGGAACCTGAGTTTTATGAGGCTATGTACACACCGCATACAGTCTTACAGGCTGTTGGGGCTTGTGTTCTTTGCAATTCACAGACTTCATTAAGATGTGGTGCTTGCATACGTAGACCATTCTTATGTTGTAAATGCTGTTACGACCATGTCATATCAACATCACATAAATTAGTCTTGTCTGTTAATCCGTATGTTTGCAATGCTCCAGGTTGTGATGTCACAGATGTGACTCAACTTTACTTAGGAGGTATGAGCTATTATTGTAAATCACATAAACCACCCATTAGTTTTCCATTGTGTGCTAATGGACAAGTTTTTGGTTTATATAAAAATACATGTGTTGGTAGCGATAATGTTACTGACTTTAATGCAATTGCAACATGTGACTGGACAAATGCTGGTGATTACATTTTAGCTAACACCTGTACTGAAAGACTCAAGCTTTTTGCAGCAGAAACGCTCAAAGCTACTGAGGAGACATTTAAACTGTCTTATGGTATTGCTACTGTACGTGAAGTGCTGTCTGACAGAGAATTACATCTTTCATGGGAAGTTGGTAAACCTAGACCACCACTTAACCGAAATTATGTCTTTACTGGTTATCGTGTAACTAAAAACAGTAAAGTACAAATAGGAGAGTACACCTTTGAAAAAGGTGACTATGGTGATGCTGTTGTTTACCGAGGTACAACAACTTACAAATTAAATGTTGGTGATTATTTTGTGCTGACATCACATACAGTAATGCCATTAAGTGCACCTACACTAGTGCCACAAGAGCACTATGTTAGAATTACTGGCTTATACCCAACACTCAATATCTCAGATGAGTTTTCTAGCAATGTTGCAAATTATCAAAAGGTTGGTATGCAAAAGTATTCTACACTCCAGGGACCACCTGGTACTGGTAAGAGTCATTTTGCTATTGGCCTAGCTCTCTACTACCCTTCTGCTCGCATAGTGTATACAGCTTGCTCTCATGCCGCTGTTGATGCACTATGTGAGAAGGCATTAAAATATTTGCCTATAGATAAATGTAGTAGAATTATACCTGCACGTGCTCGTGTAGAGTGTTTTGATAAATTCAAAGTGAATTCAACATTAGAACAGTATGTCTTTTGTACTGTAAATGCATTGCCTGAGACGACAGCAGATATAGTTGTCTTTGATGAAATTTCAATGGCCACAAATTATGATTTGAGTGTTGTCAATGCCAGATTACGTGCTAAGCACTATGTGTACATTGGCGACCCTGCTCAATTACCTGCACCACGCACATTGCTAACTAAGGGCACACTAGAACCAGAATATTTCAATTCAGTGTGTAGACTTATGAAAACTATAGGTCCAGACATGTTCCTCGGAACTTGTCGGCGTTGTCCTGCTGAAATTGTTGACACTGTGAGTGCTTTGGTTTATGATAATAAGCTTAAAGCACATAAAGACAAATCAGCTCAATGCTTTAAAATGTTTTATAAGGGTGTTATCACGCATGATGTTTCATCTGCAATTAACAGGCCACAAATAGGCGTGGTAAGAGAATTCCTTACACGTAACCCTGCTTGGAGAAAAGCTGTCTTTATTTCACCTTATAATTCACAGAATGCTGTAGCCTCAAAGATTTTGGGACTACCAACTCAAACTGTTGATTCATCACAGGGCTCAGAATATGACTATGTCATATTCACTCAAACCACTGAAACAGCTCACTCTTGTAATGTAAACAGATTTAATGTTGCTATTACCAGAGCAAAAGTAGGCATACTTTGCATAATGTCTGATAGAGACCTTTATGACAAGTTGCAATTTACAAGTCTTGAAATTCCACGTAGGAATGTGGCAACTTTACAAGCTGAAAATGTAACAGGACTCTTTAAAGATTGTAGTAAGGTAATCACTGGGTTACATCCTACACAGGCACCTACACACCTCAGTGTTGACACTAAATTCAAAACTGAAGGTTTATGTGTTGACATACCTGGCATACCTAAGGACATGACCTATAGAAGACTCATCTCTATGATGGGTTTTAAAATGAATTATCAAGTTAATGGTTACCCTAACATGTTTATCACCCGCGAAGAAGCTATAAGACATGTACGTGCATGGATTGGCTTCGATGTCGAGGGGTGTCATGCTACTAGAGAAGCTGTTGGTACCAATTTACCTTTACAGCTAGGTTTTTCTACAGGTGTTAACCTAGTTGCTGTACCTACAGGTTATGTTGATACACCTAATAATACAGATTTTTCCAGAGTTAGTGCTAAACCACCGCCTGGAGATCAATTTAAACACCTCATACCACTTATGTACAAAGGACTTCCTTGGAATGTAGTGCGTATAAAGATTGTACAAATGTTAAGTGACACACTTAAAAATCTCTCTGACAGAGTCGTATTTGTCTTATGGGCACATGGCTTTGAGTTGACATCTATGAAGTATTTTGTGAAAATAGGACCTGAGCGCACCTGTTGTCTATGTGATAGACGTGCCACATGCTTTTCCACTGCTTCAGACACTTATGCCTGTTGGCATCATTCTATTGGATTTGATTACGTCTATAATCCGTTTATGATTGATGTTCAACAATGGGGTTTTACAGGTAACCTACAAAGCAACCATGATCTGTATTGTCAAGTCCATGGTAATGCACATGTAGCTAGTTGTGATGCAATCATGACTAGGTGTCTAGCTGTCCACGAGTGCTTTGTTAAGCGTGTTGACTGGACTATTGAATATCCTATAATTGGTGATGAACTGAAGATTAATGCGGCTTGTAGAAAGGTTCAACACATGGTTGTTAAAGCTGCATTATTAGCAGACAAATTCCCAGTTCTTCACGACATTGGTAACCCTAAAGCTATTAAGTGTGTACCTCAAGCTGATGTAGAATGGAAGTTCTATGATGCACAGCCTTGTAGTGACAAAGCTTATAAAATAGAAGAATTATTCTATTCTTATGCCACACATTCTGACAAATTCACAGATGGTGTATGCCTATTTTGGAATTGCAATGTCGATAGATATCCTGCTAATTCCATTGTTTGTAGATTTGACACTAGAGTGCTATCTAACCTTAACTTGCCTGGTTGTGATGGTGGCAGTTTGTATGTAAATAAACATGCATTCCACACACCAGCTTTTGATAAAAGTGCTTTTGTTAATTTAAAACAATTACCATTTTTCTATTACTCTGACAGTCCATGTGAGTCTCATGGAAAACAAGTAGTGTCAGATATAGATTATGTACCACTAAAGTCTGCTACGTGTATAACACGTTGCAATTTAGGTGGTGCTGTCTGTAGACATCATGCTAATGAGTACAGATTGTATCTCGATGCTTATAACATGATGATCTCAGCTGGCTTTAGCTTGTGGGTTTACAAACAATTTGATACTTATAACCTCTGGAACACTTTTACAAGACTTCAGAGTTTAGAAAATGTGGCTTTTAATGTTGTAAATAAGGGACACTTTGATGGACAACAGGGTGAAGTACCAGTTTCTATCATTAATAACACTGTTTACACAAAAGTTGATGGTGTTGATGTAGAATTGTTTGAAAATAAAACAACATTACCTGTTAATGTAGCATTTGAGCTTTGGGCTAAGCGCAACATTAAACCAGTACCAGAGGTGAAAATACTCAATAATTTGGGTGTGGACATTGCTGCTAATACTGTGATCTGGGACTACAAAAGAGATGCTCCAGCACATATATCTACTATTGGTGTTTGTTCTATGACTGACATAGCCAAGAAACCAACTGAAACGATTTGTGCACCACTCACTGTCTTTTTTGATGGTAGAGTTGATGGTCAAGTAGACTTATTTAGAAATGCCCGTAATGGTGTTCTTATTACAGAAGGTAGTGTTAAAGGTTTACAACCATCTGTAGGTCCCAAACAAGCTAGTCTTAATGGAGTCACATTAATTGGAGAAGCCGTAAAAACACAGTTCAATTATTATAAGAAAGTTGATGGTGTTGTCCAACAATTACCTGAAACTTACTTTACTCAGAGTAGAAATTTACAAGAATTTAAACCCAGGAGTCAAATGGAAATTGATTTCTTAGAATTAGCTATGGATGAATTCATTGAACGGTATAAATTAGAAGGCTATGCCTTCGAACATATCGTTTATGGAGATTTTAGTCATAGTCAGTTAGGTGGTTTACATCTACTGATTGGACTAGCTAAACGTTTTAAGGAATCACCTTTTGAATTAGAAGATTTTATTCCTATGGACAGTACAGTTAAAAACTATTTCATAACAGATGCGCAAACAGGTTCATCTAAGTGTGTGTGTTCTGTTATTGATTTATTACTTGATGATTTTGTTGAAATAATAAAATCCCAAGATTTATCTGTAGTTTCTAAGGTTGTCAAAGTGACTATTGACTATACAGAAATTTCATTTATGCTTTGGTGTAAAGATGGCCATGTAGAAACATTTTACCCAAAATTACAATCTAGTCAAGCGTGGCAACCGGGTGTTGCTATGCCTAATCTTTACAAAATGCAAAGAATGCTATTAGAAAAGTGTGACCTTCAAAATTATGGTGATAGTGCAACATTACCTAAAGGCATAATGATGAATGTCGCAAAATATACTCAACTGTGTCAATATTTAAACACATTAACATTAGCTGTACCCTATAATATGAGAGTTATACATTTTGGTGCTGGTTCTGATAAAGGAGTTGCACCAGGTACAGCTGTTTTAAGACAGTGGTTGCCTACGGGTACGCTGCTTGTCGATTCAGATCTTAATGACTTTGTCTCTGATGCAGATTCAACTTTGATTGGTGATTGTGCAACTGTACATACAGCTAATAAATGGGATCTCATTATTAGTGATATGTACGACCCTAAGACTAAAAATGTTACAAAAGAAAATGACTCTAAAGAGGGTTTTTTCACTTACATTTGTGGGTTTATACAACAAAAGCTAGCTCTTGGAGGTTCCGTGGCTATAAAGATAACAGAACATTCTTGGAATGCTGATCTTTATAAGCTCATGGGACACTTCGCATGGTGGACAGCCTTTGTTACTAATGTGAATGCGTCATCATCTGAAGCATTTTTAATTGGATGTAATTATCTTGGCAAACCACGCGAACAAATAGATGGTTATGTCATGCATGCAAATTACATATTTTGGAGGAATACAAATCCAATTCAGTTGTCTTCCTATTCTTTATTTGACATGAGTAAATTTCCCCTTAAATTAAGGGGTACTGCTGTTATGTCTTTAAAAGAAGGTCAAATCAATGATATGATTTTATCTCTTCTTAGTAAAGGTAGACTTATAATTAGAGAAAACAACAGAGTTGTTATTTCTAGTGATGTTCTTGTTAACAACTAAACGAACAATGTTTGTTTTTCTTGTTTTATTGCCACTAGTCTCTAGTCAGTGTGTTAATCTTACAACCAGAACTCAATTACCCCCTGCATACACTAATTCTTTCACACGTGGTGTTTATTACCCTGACAAAGTTTTCAGATCCTCAGTTTTACATTCAACTCAGGACTTGTTCTTACCTTTCTTTTCCAATGTTACTTGGTTCCATGCTATACATGTCTCTGGGACCAATGGTACTAAGAGGTTTGATAACCCTGTCCTACCATTTAATGATGGTGTTTATTTTGCTTCCACTGAGAAGTCTAACATAATAAGAGGCTGGATTTTTGGTACTACTTTAGATTCGAAGACCCAGTCCCTACTTATTGTTAATAACGCTACTAATGTTGTTATTAAAGTCTGTGAATTTCAATTTTGTAATGATCCATTTTTGGGTGTTTATTACCACAAAAACAACAAAAGTTGGATGGAAAGTGAGTTCAGAGTTTATTCTAGTGCGAATAATTGCACTTTTGAATATGTCTCTCAGCCTTTTCTTATGGACCTTGAAGGAAAACAGGGTAATTTCAAAAATCTTAGGGAATTTGTGTTTAAGAATATTGATGGTTATTTTAAAATATATTCTAAGCACACGCCTATTAATTTAGTGCGTGATCTCCCTCAGGGTTTTTCGGCTTTAGAACCATTGGTAGATTTGCCAATAGGTATTAACATCACTAGGTTTCAAACTTTACTTGCTTTACATAGAAGTTATTTGACTCCTGGTGATTCTTCTTCAGGTTGGACAGCTGGTGCTGCAGCTTATTATGTGGGTTATCTTCAACCTAGGACTTTTCTATTAAAATATAATGAAAATGGAACCATTACAGATGCTGTAGACTGTGCACTTGACCCTCTCTCAGAAACAAAGTGTACGTTGAAATCCTTCACTGTAGAAAAAGGAATCTATCAAACTTCTAACTTTAGAGTCCAACCAACAGAATCTATTGTTAGATTTCCTAATATTACAAACTTGTGCCCTTTTGGTGAAGTTTTTAACGCCACCAGATTTGCATCTGTTTATGCTTGGAACAGGAAGAGAATCAGCAACTGTGTTGCTGATTATTCTGTCCTATATAATTCCGCATCATTTTCCACTTTTAAGTGTTATGGAGTGTCTCCTACTAAATTAAATGATCTCTGCTTTACTAATGTCTATGCAGATTCATTTGTAATTAGAGGTGATGAAGTCAGACAAATCGCTCCAGGGCAAACTGGAAAGATTGCTGATTATAATTATAAATTACCAGATGATTTTACAGGCTGCGTTATAGCTTGGAATTCTAACAATCTTGATTCTAAGGTTGGTGGTAATTATAATTACCTGTATAGATTGTTTAGGAAGTCTAATCTCAAACCTTTTGAGAGAGATATTTCAACTGAAATCTATCAGGCCGGTAGCACACCTTGTAATGGTGTTGAAGGTTTTAATTGTTACTTTCCTTTACAATCATATGGTTTCCAACCCACTAATGGTGTTGGTTACCAACCATACAGAGTAGTAGTACTTTCTTTTGAACTTCTACATGCACCAGCAACTGTTTGTGGACCTAAAAAGTCTACTAATTTGGTTAAAAACAAATGTGTCAATTTCAACTTCAATGGTTTAACAGGCACAGGTGTTCTTACTGAGTCTAACAAAAAGTTTCTGCCTTTCCAACAATTTGGCAGAGACATTGCTGACACTACTGATGCTGTCCGTGATCCACAGACACTTGAGATTCTTGACATTACACCATGTTCTTTTGGTGGTGTCAGTGTTATAACACCAGGAACAAATACTTCTAACCAGGTTGCTGTTCTTTATCAGGATGTTAACTGCACAGAAGTCCCTGTTGCTATTCATGCAGATCAACTTACTCCTACTTGGCGTGTTTATTCTACAGGTTCTAATGTTTTTCAAACACGTGCAGGCTGTTTAATAGGGGCTGAACATGTCAACAACTCATATGAGTGTGACATACCCATTGGTGCAGGTATATGCGCTAGTTATCAGACTCAGACTAATTCTCCTCGGCGGGCACGTAGTGTAGCTAGTCAATCCATCATTGCCTACACTATGTCACTTGGTGCAGAAAATTCAGTTGCTTACTCTAATAACTCTATTGCCATACCCACAAATTTTACTATTAGTGTTACCACAGAAATTCTACCAGTGTCTATGACCAAGACATCAGTAGATTGTACAATGTACATTTGTGGTGATTCAACTGAATGCAGCAATCTTTTGTTGCAATATGGCAGTTTTTGTACACAATTAAACCGTGCTTTAACTGGAATAGCTGTTGAACAAGACAAAAACACCCAAGAAGTTTTTGCACAAGTCAAACAAATTTACAAAACACCACCAATTAAAGATTTTGGTGGTTTTAATTTTTCACAAATATTACCAGATCCATCAAAACCAAGCAAGAGGTCATTTATTGAAGATCTACTTTTCAACAAAGTGACACTTGCAGATGCTGGCTTCATCAAACAATATGGTGATTGCCTTGGTGATATTGCTGCTAGAGACCTCATTTGTGCACAAAAGTTTAACGGCCTTACTGTTTTGCCACCTTTGCTCACAGATGAAATGATTGCTCAATACACTTCTGCACTGTTAGCGGGTACAATCACTTCTGGTTGGACCTTTGGTGCAGGTGCTGCATTACAAATACCATTTGCTATGCAAATGGCTTATAGGTTTAATGGTATTGGAGTTACACAGAATGTTCTCTATGAGAACCAAAAATTGATTGCCAACCAATTTAATAGTGCTATTGGCAAAATTCAAGACTCACTTTCTTCCACAGCAAGTGCACTTGGAAAACTTCAAGATGTGGTCAACCAAAATGCACAAGCTTTAAACACGCTTGTTAAACAACTTAGCTCCAATTTTGGTGCAATTTCAAGTGTTTTAAATGATATCCTTTCACGTCTTGACAAAGTTGAGGCTGAAGTGCAAATTGATAGGTTGATCACAGGCAGACTTCAAAGTTTGCAGACATATGTGACTCAACAATTAATTAGAGCTGCAGAAATCAGAGCTTCTGCTAATCTTGCTGCTACTAAAATGTCAGAGTGTGTACTTGGACAATCAAAAAGAGTTGATTTTTGTGGAAAGGGCTATCATCTTATGTCCTTCCCTCAGTCAGCACCTCATGGTGTAGTCTTCTTGCATGTGACTTATGTCCCTGCACAAGAAAAGAACTTCACAACTGCTCCTGCCATTTGTCATGATGGAAAAGCACACTTTCCTCGTGAAGGTGTCTTTGTTTCAAATGGCACACACTGGTTTGTAACACAAAGGAATTTTTATGAACCACAAATCATTACTACAGACAACACATTTGTGTCTGGTAACTGTGATGTTGTAATAGGAATTGTCAACAACACAGTTTATGATCCTTTGCAACCTGAATTAGACTCATTCAAGGAGGAGTTAGATAAATATTTTAAGAATCATACATCACCAGATGTTGATTTAGGTGACATCTCTGGCATTAATGCTTCAGTTGTAAACATTCAAAAAGAAATTGACCGCCTCAATGAGGTTGCCAAGAATTTAAATGAATCTCTCATCGATCTCCAAGAACTTGGAAAGTATGAGCAGTATATAAAATGGCCATGGTACATTTGGCTAGGTTTTATAGCTGGCTTGATTGCCATAGTAATGGTGACAATTATGCTTTGCTGTATGACCAGTTGCTGTAGTTGTCTCAAGGGCTGTTGTTCTTGTGGATCCTGCTGCAAATTTGATGAAGACGACTCTGAGCCAGTGCTCAAAGGAGTCAAATTACATTACACATAAACGAACTTATGGATTTGTTTATGAGAATCTTCACAATTGGAACTGTAACTTTGAAGCAAGGTGAAATCAAGGATGCTACTCCTTCAGATTTTGTTCGCGCTACTGCAACGATACCGATACAAGCCTCACTCCCTTTCGGATGGCTTATTGTTGGCGTTGCACTTCTTGCTGTTTTTCAGAGCGCTTCCAAAATCATAACCCTCAAAAAGAGATGGCAACTAGCACTCTCCAAGGGTGTTCACTTTGTTTGCAACTTGCTGTTGTTGTTTGTAACAGTTTACTCACACCTTTTGCTCGTTGCTGCTGGCCTTGAAGCCCCTTTTCTCTATCTTTATGCTTTAGTCTACTTCTTGCAGAGTATAAACTTTGTAAGAATAATAATGAGGCTTTGGCTTTGCTGGAAATGCCGTTCCAAAAACCCATTACTTTATGATGCCAACTATTTTCTTTGCTGGCATACTAATTGTTACGACTATTGTATACCTTACAATAGTGTAACTTCTTCAATTGTCATTACTTCAGGTGATGGCACAACAAGTCCTATTTCTGAACATGACTACCAGATTGGTGGTTATACTGAAAAATGGGAATCTGGAGTAAAAGACTGTGTTGTATTACACAGTTACTTCACTTCAGACTATTACCAGCTGTACTCAACTCAATTGAGTACAGACACTGGTGTTGAACATGTTACCTTCTTCATCTACAATAAAATTGTTGATGAGCCTGAAGAACATGTCCAAATTCACACAATCGACGGTTCATCCGGAGTTGTTAATCCAGTAATGGAACCAATTTATGATGAACCGACGACGACTACTAGCGTGCCTTTGTAAGCACAAGCTGATGAGTACGAACTTATGTACTCATTCGTTTCGGAAGAGACAGGTACGTTAATAGTTAATAGCGTACTTCTTTTTCTTGCTTTCGTGGTATTCTTGCTAGTTACACTAGCCATCCTTACTGCGCTTCGATTGTGTGCGTACTGCTGCAATATTGTTAACGTGAGTCTTGTAAAACCTTCTTTTTACGTTTACTCTCGTGTTAAAAATCTGAATTCTTCTAGAGTTCCTGATCTTCTGGTCTAAACGAACTAAATATTATATTAGTTTTTCTGTTTGGAACTTTAATTTTAGCCATGGCAGATTCCAACGGTACTATTACCGTTGAAGAGCTTAAAAAGCTCCTTGAACAATGGAACCTAGTAATAGGTTTCCTATTCCTTACATGGATTTGTCTTCTACAATTTGCCTATGCCAACAGGAATAGGTTTTTGTATATAATTAAGTTAATTTTCCTCTGGCTGTTATGGCCAGTAACTTTAGCTTGTTTTGTGCTTGCTGCTGTTTACAGAATAAATTGGATCACCGGTGGAATTGCTATCGCAATGGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTTTGCGCGTACGCGTTCCATGTGGTCATTCAATCCAGAAACTAACATTCTTCTCAACGTGCCACTCCATGGCACTATTCTGACCAGACCGCTTCTAGAAAGTGAACTCGTAATCGGAGCTGTGATCCTTCGTGGACATCTTCGTATTGCTGGACACCATCTAGGACGCTGTGACATCAAGGACCTGCCTAAAGAAATCACTGTTGCTACATCACGAACGCTTTCTTATTACAAATTGGGAGCTTCGCAGCGTGTAGCAGGTGACTCAGGTTTTGCTGCATACAGTCGCTACAGGATTGGCAACTATAAATTAAACACAGACCATTCCAGTAGCAGTGACAATATTGCTTTGCTTGTACAGTAAGTGACAACAGATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGATTAAACGAACATGAAAATTATTCTTTTCTTGGCACTGATAACACTCGCTACTTGTGAGCTTTATCACTACCAAGAGTGTGTTAGAGGTACAACAGTACTTTTAAAAGAACCTTGCTCTTCTGGAACATACGAGGGCAATTCACCATTTCATCCTCTAGCTGATAACAAATTTGCACTGACTTGCTTTAGCACTCAATTTGCTTTTGCTTGTCCTGACGGCGTAAAACACGTCTATCAGTTACGTGCCAGATCAGTTTCACCTAAACTGTTCATCAGACAAGAGGAAGTTCAAGAACTTTACTCTCCAATTTTTCTTATTGTTGCGGCAATAGTGTTTATAACACTTTGCTTCACACTCAAAAGAAAGACAGAATGATTGAACTTTCATTAATTGACTTCTATTTGTGCTTTTTAGCCTTTCTGCTATTCCTTGTTTTAATTATGCTTATTATCTTTTGGTTCTCACTTGAACTGCAAGATCATAATGAAACTTGTCACGCCTAAACGAACATGAAATTTCTTGTTTTCTTAGGAATCATCACAACTGTAGCTGCATTTCACCAAGAATGTAGTTTACAGTCATGTACTCAACATCAACCATATGTAGTTGATGACCCGTGTCCTATTCACTTCTATTCTAAATGGTATATTAGAGTAGGAGCTAGAAAATCAGCACCTTTAATTGAATTGTGCGTGGATGAGGCTGGTTCTAAATCACCCATTCAGTACATCGATATCGGTAATTATACAGTTTCCTGTTTACCTTTTACAATTAATTGCCAGGAACCTAAATTGGGTAGTCTTGTAGTGCGTTGTTCGTTCTATGAAGACTTTTTAGAGTATCATGACGTTCGTGTTGTTTTAGATTTCATCTAAACGAACAAACTAAAATGTCTGATAATGGACCCCAAAATCAGCGAAATGCACCCCGCATTACGTTTGGTGGACCCTCAGATTCAACTGGCAGTAACCAGAATGGAGAACGCAGTGGGGCGCGATCAAAACAACGTCGGCCCCAAGGTTTACCCAATAATACTGCGTCTTGGTTCACCGCTCTCACTCAACATGGCAAGGAAGACCTTAAATTCCCTCGAGGACAAGGCGTTCCAATTAACACCAATAGCAGTCCAGATGACCAAATTGGCTACTACCGAAGAGCTACCAGACGAATTCGTGGTGGTGACGGTAAAATGAAAGATCTCAGTCCAAGATGGTATTTCTACTACCTAGGAACTGGGCCAGAAGCTGGACTTCCCTATGGTGCTAACAAAGACGGCATCATATGGGTTGCAACTGAGGGAGCCTTGAATACACCAAAAGATCACATTGGCACCCGCAATCCTGCTAACAATGCTGCAATCGTGCTACAACTTCCTCAAGGAACAACATTGCCAAAAGGCTTCTACGCAGAAGGGAGCAGAGGCGGCAGTCAAGCCTCTTCTCGTTCCTCATCACGTAGTCGCAACAGTTCAAGAAATTCAACTCCAGGCAGCAGTAGGGGAACTTCTCCTGCTAGAATGGCTGGCAATGGCGGTGATGCTGCTCTTGCTTTGCTGCTGCTTGACAGATTGAACCAGCTTGAGAGCAAAATGTCTGGTAAAGGCCAACAACAACAAGGCCAAACTGTCACTAAGAAATCTGCTGCTGAGGCTTCTAAGAAGCCTCGGCAAAAACGTACTGCCACTAAAGCATACAATGTAACACAAGCTTTCGGCAGACGTGGTCCAGAACAAACCCAAGGAAATTTTGGGGACCAGGAACTAATCAGACAAGGAACTGATTACAAACATTGGCCGCAAATTGCACAATTTGCCCCCAGCGCTTCAGCGTTCTTCGGAATGTCGCGCATTGGCATGGAAGTCACACCTTCGGGAACGTGGTTGACCTACACAGGTGCCATCAAATTGGATGACAAAGATCCAAATTTCAAAGATCAAGTCATTTTGCTGAATAAGCATATTGACGCATACAAAACATTCCCACCAACAGAGCCTAAAAAGGACAAAAAGAAGAAGGCTGATGAAACTCAAGCCTTACCGCAGAGACAGAAGAAACAGCAAACTGTGACTCTTCTTCCTGCTGCAGATTTGGATGATTTCTCCAAACAATTGCAACAATCCATGAGCAGTGCTGACTCAACTCAGGCCTAAACTCATGCAGACCACACAAGGCAGATGGGCTATATAAACGTTTTCGCTTTTCCGTTTACGATATATAGTCTACTCTTGTGCAGAATGAATTCTCGTAACTACATAGCACAAGTAGATGTAGTTAACTTTAATCTCACATAGCAATCTTTAATCAGTGTGTAACATTAGGGAGGACTTGAAAGAGCCACCACATTTTCACCGAGGCCACGCGGAGTACGATCGAGTGTACAGTGAACAATGCTAGGGAGAGCTGCCTATATGGAAGAGCCCTAATGTGTAAAATTAATTTTAGTAGTGCTATCCCCATGTGATTTTAATAGCTTCTTAGGAGAATGACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA'] + ] + # 0-based gene coordinates + # from, to, name, within gene codon offset (to deal with ORF1a/b overlap) + self.gene_coordinates = [[265, 13482, 'ORF1a', 0], + [13467, 21554, 'ORF1b', -1], + [21562, 25383, 'S', 0], + [25392, 26219, 'ORF3a', 0], + [26244, 26471, 'E', 0], + [26522, 27190, 'M', 0], + [27201, 27386, 'ORF6', 0], + [27393, 27758, 'ORF7a', 0], + [27893, 28258, 'ORF8', 0], + [28273, 29532, 'N', 0], + [29557, 29673, 'ORF10', 0]] + self.score_matrix_ = BioExt.scorematrices.DNA95.load() + if summary_json is not None: + self.summary_json = summary_json + if annotation_json is not None: + self.annotation_json = annotation_json + try: + if arguments.summary_input: + with open(arguments.summary_input) as fh: + self.summary_json = json.load(fh) + except Exception: + pass + try: + if arguments.annotation_input: + with open(arguments.annotation_input) as fh: + self.annotation_json = json.load(fh) + except Exception: + pass + self.gene = self.arguments.gene + self._get_incoming_labels() + self._get_map() + + def summary(self): + try: + if self.summary_json is not None: + if self.gene not in self.summary_json: + self.summary_json[self.gene] = {} + if self.cfel is not None: + self.cfel_summary() + if self.relax is not None: + self.relax_summary() + if self.busted is not None: + self.busted_summary() + if self.slac is not None: + self.slac_summary() + if self.fel is not None: + self.fel_summary() + if self.meme is not None: + self.meme_summary() + if self.meme_full is not None: + self.meme_full_summary() + if self.prime is not None: + self.prime_summary() + if self.fade is not None: + self.fade_summary() + if self.bgm is not None: + self.bgm_summary() + except Exception: + if self.gene: + del self.summary_json[self.gene] + if self.gene in self.annotation_json: + del self.annotation_json[self.gene] + raise + return self.annotation_json, self.summary_json + + def cfel_summary(self): + self.cfel = self._load_json(self.arguments.cfel) + if self.cfel is None: + return + node_tags = {} + _ = self._newick_parser(self.cfel['input']['trees']['0'], False, node_tags, self.cfel)['json'] + if self.summary_json is not None: + omegas = {} + T = {} + for k in [[k.split('*')[1], v[0][0]] for k, v in self.cfel['fits']['Global MG94xREV']['Rate Distributions'].items()]: + if k[0] != 'background': + self.test_map[k[0]] = 'Test' + else: + self.test_map[k[0]] = 'Reference' + omegas[k[0]] = k[1] + T[k[0]] = 0. + for branch, nt in (self.cfel['tested']['0']).items(): + if branch not in node_tags: + node_tags[branch] = [] + info = self.cfel['branch attributes']['0'][branch] + if nt != '': + T[nt] += info['Global MG94xREV'] + node_tags[branch].append(info['Global MG94xREV']) + self.summary_json[self.gene]['rates'] = {'mean-omega': omegas, 'T': T} + beta_indices = [] + p_indices = [] + subs = [] + for i, tag in enumerate(self.cfel['MLE']['headers']): + if tag[0].find('beta') == 0: + beta_indices.append([i, re.split(r'\(|\)', tag[0])[1]]) + elif tag[0].find('P-value') == 0: + p_indices.append([i, re.split(r'\(|\)|for ', tag[0])[1]]) + elif tag[0].find('subs') == 0: + subs.append([i, re.split(r'\(|\)', tag[0])[1]]) + for i, row in enumerate(self.cfel['MLE']['content']['0']): + if self.annotation_json is not None and len(self.ref_map): # if this is specified, write everything out + gs = self._get_genomic_annotation(i) + if gs[0] >= 0: + self.include_in_annotation[i] = gs[0] + self.annotation_json[gs[0]] = { + 'G': gs[1], + 'S': gs[2], + 'index': i, + 'bCFEL': { + 'p': row[4], + 'a': row[0], + 'b': self._make_report_dict(row, beta_indices), + 'pi': self._make_report_dict(row, p_indices), + 'pp': row[-2], + 's': self._make_report_dict(row, subs), + 'q': row[-3] + } + } + if row[-4] <= self.arguments.pvalue: + self.site_reports[i] = {'cfel': row} + + def relax_summary(self): + self.relax = self._load_json(self.arguments.relax) + if self.relax is None: + return + if self.summary_json is not None: + relax_d = {} + for r, rr in self.summary_json[self.gene]['rates']['mean-omega'].items(): + relax_d[r] = [] + for ignored, rd in self.relax['fits']['RELAX alternative']['Rate Distributions'][self.test_map[r]].items(): + relax_d[r].append(rd) + self.summary_json[self.gene]['rates']['relax'] = relax_d + self.summary_json[self.gene]['relax'] = { + 'p': self.relax['test results']['p-value'], + 'K': self.relax['test results']['relaxation or intensification parameter'] + } + + def busted_summary(self): + self.busted = self._load_json(self.arguments.busted) + if self.busted is None: + return + if self.summary_json is not None: + self.summary_json[self.gene]['rates']['busted'] = self.busted['fits']['Unconstrained model']['Rate Distributions'] + self.summary_json[self.gene]['busted'] = {'p': self.busted['test results']['p-value'], } + + def slac_summary(self): + self.slac = self._load_json(self.arguments.slac) + if self.slac is None: + return + + def def_value(): + return defaultdict(int) + compressed_subs = {} + node_tags = {} + the_tree = self._newick_parser(self.slac['input']['trees']['0'], False, node_tags, self.slac)['json'] + root_node = None + if self.summary_json is not None: + for branch, info in self.slac['branch attributes']['0'].items(): + if branch in node_tags: + node_tags[branch].append(info['Global MG94xREV']) + else: + root_node = branch + self.summary_json[self.gene]['tree'] = self.slac['input']['trees']['0'] + self.summary_json[self.gene]['tree_tags'] = node_tags + if len(self.include_in_annotation): + for i in self.include_in_annotation: + report = self.annotation_json[self.include_in_annotation[i]] + counts_codon_site = {} + counts_aa_site = {} + gs = self._get_genomic_annotation(i) + if gs[0] >= 0: + self.labels[root_node] = self.slac['branch attributes']['0'][root_node]['codon'][0][i] + try: + self._traverse_tree_in_order(the_tree, self.slac['branch attributes']['0'], i, None, root_node) + except Exception: + raise + compressed_subs[gs[0]] = self.labels + for k in set([k[0] for k in node_tags.values()]): + if len(k): + counts_codon_site[k] = defaultdict(int) + counts_aa_site[k] = defaultdict(int) + for branch, tag in node_tags.items(): + if len(tag[0]) > 0 and tag[1] is False: + codon = self.slac['branch attributes']['0'][branch]['codon'][0][i] + aa = self.slac['branch attributes']['0'][branch]['amino-acid'][0][i] + counts_codon_site[tag[0]][codon] += 1 + counts_aa_site[tag[0]][aa] += 1 + report['cdn'] = counts_codon_site + report['aa'] = counts_aa_site + self.summary_json[self.gene]['subs'] = compressed_subs + + def fel_summary(self): + self.fel = self._load_json(self.arguments.fel) + if None in [self.fel, self.cfel]: + return + for i, row in enumerate(self.fel['MLE']['content']['0']): + if i in self.include_in_annotation: + self.annotation_json[self.include_in_annotation[i]]['bFEL'] = {'a': row[0], 'b': row[1], 'p': row[4]} + if i in self.site_reports or row[4] <= self.arguments.pvalue and row[1] > row[0]: + if i in self.site_reports: + self.site_reports[i]['fel'] = row + else: + self.site_reports[i] = {'fel': row, + 'cfel': self.cfel['MLE']['content']['0'][i]} + + def meme_summary(self): + self.meme = self._load_json(self.arguments.meme) + if None in [self.fel, self.cfel, self.meme]: + return + for i, row in enumerate(self.meme['MLE']['content']['0']): + if i in self.include_in_annotation: + self.annotation_json[self.include_in_annotation[i]]['bMEME'] = { + 'p': row[6], + 'a': row[0], + 'b+': row[3], + 'w+': row[4], + 'b-': row[1], + 'w-': row[2], + 'br': row[7] + } + if i in self.site_reports or row[6] <= self.arguments.pvalue: + if i in self.site_reports: + self.site_reports[i]['meme'] = row + else: + self.site_reports[i] = {'meme': row, + 'fel': self.fel['MLE']['content']['0'][i], + 'cfel': self.cfel['MLE']['content']['0'][i]} + # annotate branches with EBF support + for n, info in self.meme['branch attributes']['0'].items(): + + if n in self.summary_json[self.gene]['tree_tags']: + sig_sites = [] + for tag, ebf in info.items(): + bits = tag.split(' ') + if len(bits) >= 4 and ebf >= 100: + sig_sites.append(self.include_in_annotation[int(bits[2]) - 1]) + self.summary_json[self.gene]['tree_tags'][n].append(sig_sites) + + def meme_full_summary(self): + self.meme_full = self._load_json(self.arguments.meme_full) + if None in [self.fel, self.cfel, self.meme, self.meme_full]: + return + for i, row in enumerate(self.meme_full['MLE']['content']['0']): + if i in self.include_in_annotation: + self.annotation_json[self.include_in_annotation[i]]['lMEME'] = { + 'p': row[6], + 'a': row[0], + 'b+': row[3], + 'w+': row[4], + 'b-': row[1], + 'w-': row[2], + 'br': row[7] + } + if i in self.site_reports or row[6] <= self.arguments.pvalue: + if i in self.site_reports: + self.site_reports[i]['full-meme'] = row + else: + self.site_reports[i] = {'full-meme': row, + 'meme': self.meme['MLE']['content']['0'][i], + 'fel': self.fel['MLE']['content']['0'][i], + 'cfel': self.cfel['MLE']['content']['0'][i]} + # annotate branches with EBF support + for n, info in self.meme_full['branch attributes']['0'].items(): + if n in self.summary_json[self.gene]['tree_tags']: + sig_sites = [] + for tag, ebf in info.items(): + bits = tag.split(' ') + if len(bits) >= 4 and ebf >= 100: + sig_sites.append(self.include_in_annotation[int(bits[2]) - 1]) + self.summary_json[self.gene]['tree_tags'][n].append(sig_sites) + + def prime_summary(self): + self.prime = self._load_json(self.arguments.prime) + if self.prime is None: + return + if self.summary_json is not None: + h = self.prime['MLE']['headers'] + self.summary_json[self.gene]['prime-properties'] = [h[k][1].replace('Importance for ', '') for k in range(6, len(h), 3)] + if len(self.include_in_annotation): + for i in self.include_in_annotation: + report = self.annotation_json[self.include_in_annotation[i]] + prime_info = self.prime['MLE']['content']['0'][i] + if prime_info: + report['prime'] = { + 'p': [prime_info[k] for k in ([5, ] + list(range(7, len(prime_info), 3)))], + 'lambda': [prime_info[k] for k in range(6, len(prime_info), 3)] + } + else: + report['prime'] = None # invariable + + def fade_summary(self): + self.fade = self._load_json(self.arguments.fade) + if self.fade is None: + return + if len(self.include_in_annotation): + for i in self.include_in_annotation: + report = self.annotation_json[self.include_in_annotation[i]] + report['fade'] = {} + for residue, info in self.fade['MLE']['content'].items(): + if len(residue) == 1: + report['fade'][residue] = {'rate': info['0'][i][1], 'BF': info['0'][i][-1]} + + def bgm_summary(self): + self.bgm = self._load_json(self.arguments.bgm) + if self.bgm is None: + return + if self.summary_json is not None: + try: + self.summary_json[self.gene]['bgm'] = self.bgm['MLE']['content'] + except KeyError: + self.summary_json[self.gene]['bgm'] = [] + + def _load_json(self, filename): + if filename is None: + return None + try: + with open(filename, 'r') as fh: + return json.load(fh) + except Exception: + raise + + def _get_map(self): + for seq_record in SeqIO.parse(self.arguments.combined, 'fasta'): + seq_id = seq_record.description + ref_seq_re = re.compile(self.arguments.name) + if ref_seq_re.search(seq_id): + ref_seq = str(seq_record.seq).upper() + self.aligned_str = None + + def output_record(x): + listified_input = list(x) + if len(listified_input) == 1: + self.aligned_str = listified_input[0] + + def ignore_record(x): + pass + for s in self.ref_genes: + _align_par(SeqRecord(Seq(s[1]), id=s[0]), [SeqRecord(Seq(ref_seq), id='ref')], + self.score_matrix_, False, False, 0.8, ignore_record, output_record) + if (self.aligned_str is not None): + break + self.ref_map = self.aligned_str.seq.strip('-') + c = 0 + i = 0 + map_to_genome = [] + while i < len(self.ref_map): + if self.ref_map[i:i + 3] != '---': + map_to_genome.append(i) + i += 3 + i = 0 + c = 0 + while i < len(ref_seq): + if ref_seq[i:i + 3] != '---': + self.ref_seq_map.append(map_to_genome[c // 3] + self.aligned_str.annotations['position']) + c += 3 + else: + self.ref_seq_map.append(-1) + i += 3 + if self.summary_json is not None: + if self.gene not in self.summary_json: + self.summary_json[self.gene] = dict() + self.summary_json[self.gene]['map'] = self.ref_seq_map + + def _make_report_dict(self, row, indices): + result = {} + for i, t in indices: + result[t] = row[i] + return result + + def _get_genomic_annotation(self, site): + genomic_site_coord = -1 + gene_name = '' + gene_site = -1 + if len(self.ref_seq_map): + genomic_site_coord = self.ref_seq_map[site] + if genomic_site_coord < 0: + gene_site = 'Not in SC2 (deletion)' + else: + gene_name = None + for k in self.gene_coordinates: + if k[0] <= genomic_site_coord and k[1] > genomic_site_coord: + genomic_site = ((genomic_site_coord + k[3]) - k[0]) // 3 + gene_name = k[2] + gene_site = genomic_site + 1 + break + if gene_name is None: + gene_name = 'Not mapped' + else: + gene_name = 'N/A' + return (genomic_site_coord, gene_name, gene_site) + + def _traverse_tree_in_order(self, node, slac_data, i, parent_tag, root): + node_tag = None + if node is None: + return + try: + nn = root if node['name'] == 'root' else node['name'] + except Exception: + raise + if nn in slac_data: + node_tag = slac_data[nn]['codon'][0][i] + if (parent_tag != node_tag): + self.labels[nn] = node_tag + self.labels[node['name']] = node_tag + if 'children' in node: + for c in node['children']: + if c is not None: + if 'name' in c: + self._traverse_tree_in_order(c, slac_data, i, node_tag, root) + + def _match_node_names(self, qry_node, ref_node, mapping): + if 'children' in qry_node and 'children' in ref_node: + mapping[ref_node['name']] = qry_node['name'] + if len(qry_node['children']) != len(ref_node['children']): + raise Exception('Internal topology mismatch') + for i, n in enumerate(ref_node['children']): + self._match_node_names(qry_node['children'][i], n, mapping) + elif 'children' in qry_node: + raise Exception('Topology mismatch') + elif 'children' in ref_node: + raise Exception('Topology mismatch') + else: + if qry_node['name'] != ref_node['name']: + raise Exception('Leaf name mismatch') + + def _get_incoming_labels(self): + json_data = self._load_json(self.arguments.labels) + self.incoming_labels = json_data + + def _newick_parser(self, nwk_str, bootstrap_values, track_tags, json_map): + clade_stack = [] + automaton_state = 0 + current_node_name = '' + current_node_attribute = '' + current_node_annotation = '' + quote_delimiter = None + name_quotes = {"'": 1, '"': 1} + + def add_new_tree_level(): + new_level = {'name': None} + the_parent = clade_stack[len(clade_stack) - 1] + if ('children' not in the_parent): + the_parent['children'] = [] + clade_stack.append(new_level) + the_parent['children'].append(clade_stack[len(clade_stack) - 1]) + clade_stack[len(clade_stack) - 1]['original_child_order'] = len(the_parent['children']) + + def finish_node_definition(): + nonlocal current_node_name + nonlocal current_node_annotation + nonlocal current_node_attribute + this_node = clade_stack.pop() + if (bootstrap_values and 'children' in this_node): + this_node['bootstrap_values'] = current_node_name + else: + this_node['name'] = current_node_name + this_node['attribute'] = current_node_attribute + this_node['annotation'] = current_node_annotation + try: + if 'children' not in this_node: + node_tag = self.arguments.default_tag + if json_map: + tn = json_map['branch attributes']['0'][this_node['name']] + else: + tn = this_node + nn = tn['original name'] if 'original name' in tn else tn['name'] + for k, v in self.incoming_labels.items(): + if nn.find(k) >= 0: + node_tag = v + break + else: + counts = {} + node_tag = '' + for n in this_node['children']: + counts[n['tag']] = 1 + (counts[n['tag']] if n['tag'] in counts else 0) + if len(counts) == 1: + node_tag = list(counts.keys())[0] + this_node['tag'] = node_tag + except Exception: + raise + if track_tags is not None: + track_tags[this_node['name']] = [this_node['tag'], 'children' in this_node] + current_node_name = '' + current_node_attribute = '' + current_node_annotation = '' + + def generate_error(location): + unexpected = nwk_str[location] + before = nwk_str[location - 20:location + 1] + after = nwk_str[location + 1:location + 20] + return { + 'json': None, + 'error': 'Unexpected %s in %s [ERROR HERE] %s' % (unexpected, before, after) + } + tree_json = {'name': 'root'} + clade_stack.append(tree_json) + space = re.compile(r'\s') + for char_index in range(len(nwk_str)): + try: + current_char = nwk_str[char_index] + if automaton_state == 0: + # look for the first opening parenthesis + if (current_char == '('): + add_new_tree_level() + automaton_state = 1 + elif automaton_state == 1 or automaton_state == 3: + # case 1: // name + # case 3: { // branch length + # reading name + if (current_char == ':'): + automaton_state = 3 + elif current_char == ',' or current_char == ')': + try: + finish_node_definition() + automaton_state = 1 + if (current_char == ','): + add_new_tree_level() + except Exception: + return generate_error(char_index) + elif (current_char == '('): + if len(current_node_name) > 0: + return generate_error(char_index) + else: + add_new_tree_level() + elif (current_char in name_quotes): + if automaton_state == 1 and len(current_node_name) == 0 and len(current_node_attribute) == 0 and len(current_node_annotation) == 0: + automaton_state = 2 + quote_delimiter = current_char + continue + return generate_error(char_index) + else: + if (current_char == '['): + if len(current_node_annotation): + return generate_error(char_index) + else: + automaton_state = 4 + else: + if (automaton_state == 3): + current_node_attribute += current_char + else: + if (space.search(current_char)): + continue + if (current_char == ';'): + char_index = len(nwk_str) + break + current_node_name += current_char + elif automaton_state == 2: + # inside a quoted expression + if (current_char == quote_delimiter): + if (char_index < len(nwk_str - 1)): + if (nwk_str[char_index + 1] == quote_delimiter): + char_index += 1 + current_node_name += quote_delimiter + continue + quote_delimiter = 0 + automaton_state = 1 + continue + else: + current_node_name += current_char + elif automaton_state == 4: + # inside a comment / attribute + if (current_char == ']'): + automaton_state = 3 + else: + if (current_char == '['): + return generate_error(char_index) + current_node_annotation += current_char + except Exception: + return generate_error(char_index) + + if (len(clade_stack) != 1): + return generate_error(len(nwk_str) - 1) + + if (len(current_node_name)): + tree_json['name'] = current_node_name + + return { + 'json': tree_json, + 'error': None + } + + +if __name__ == '__main__': + parser = argparse.ArgumentParser(description='Summarize selection analysis results.') + parser.add_argument('--combined', help='Combined reference and query alignment from TN-93', required=False, type=str) + parser.add_argument('--pvalue', help='p-value to use', required=False, type=float, default=0.05) + parser.add_argument('--gene', help='Name of the gene or sequence being analyzed', required=False, type=str) + parser.add_argument('--labels', help='JSON file with labels', required=False, type=str) + parser.add_argument('--annotation-output', help='Write a JSON file with site annotations', required=True, type=str) + parser.add_argument('--summary-output', help='Write a JSON file here segment annotations', required=True, type=str) + parser.add_argument('--annotation-inputs', help='Comma-separated list of site annotation files to merge', required=False, type=str) + parser.add_argument('--summary-inputs', help='Comma-separated list of segment annotation files to merge', required=False, type=str) + parser.add_argument('--default-tag', help='Default name for sequences that have no explicit label', required=False, type=str, default='Reference') + parser.add_argument('--name', help='The sequence ID to highlight', required=False, default='MN908947') + parser.add_argument('--mode', help='Operation mode, generate a summary or merge multiple summaries', type=str, choices=['summary', 'merge'], default='summary') + parser.add_argument('--relax', help='Path to RELAX.json file', required=False, type=str) + parser.add_argument('--busted', help='Path to BUSTED.json file', required=False, type=str) + parser.add_argument('--slac', help='Path to SLAC.json file', required=False, type=str) + parser.add_argument('--fel', help='Path to FEL.json file', required=False, type=str) + parser.add_argument('--cfel', help='Path to CFEL.json file', required=False, type=str) + parser.add_argument('--meme', help='Path to MEME.json file', required=False, type=str) + parser.add_argument('--meme-full', help='Path to MEME-full.json file', dest='meme_full', required=False, type=str) + parser.add_argument('--prime', help='Path to PRIME.json file', required=False, type=str) + parser.add_argument('--fade', help='Path to FADE.json file', required=False, type=str) + parser.add_argument('--bgm', help='Path to BGM.json file', required=False, type=str) + arguments = parser.parse_args() + if arguments.mode == 'summary': + analyzer = HyPhySummary(arguments) + annotation_json, summary_json = analyzer.summary() + if annotation_json is not None: + with open(arguments.annotation_output, 'w') as fh: + json.dump(annotation_json, fh, indent=1) + if summary_json is not None: + with open(arguments.summary_output, 'w') as fh: + json.dump(summary_json, fh, indent=1) + else: + summary = {} + annotation = {} + for filename in arguments.annotation_inputs.split(','): + with open(filename, 'r') as fh: + annotation.update(json.load(fh)) + for filename in arguments.summary_inputs.split(','): + with open(filename, 'r') as fh: + summary.update(json.load(fh)) + with open(arguments.annotation_output, 'w') as fh: + json.dump(annotation, fh, indent=1) + with open(arguments.summary_output, 'w') as fh: + json.dump(summary, fh, indent=1) + exit(0) diff -r 5e8d0e777033 -r 60eec78ee26f test-data/summary/ORF6-segment.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/ORF6-segment.json Wed Jun 09 07:00:42 2021 +0000 @@ -0,0 +1,7 @@ +{ + "ORF6": { + "map": [], + "tree": 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+ } + }, + "settings":{ + "bayes factor":100, + "burn-in":1000000, + "chain-length":2000000, + "chains":1, + "concentration":0.5, + "grid size":20, + "method":"Variational-Bayes", + "samples":100 + }, + "site annotations":{ + "headers":{ + "Composition":"Amino acid composition of site", + "Substitutions":"Substitution history on selected branches" + }, + "site annotations":{ + "0": [ +["M12", ""], + ["F12", ""], + ["H12", ""], + ["L12", ""], + ["V12", ""], + ["D11,G1", "D->G(1)"], + ["F12", ""], + ["H1,Q11", "Q->H(1)"], + ["V12", ""], + ["T12", ""], + ["I12", ""], + ["A12", ""], + ["E12", ""], + ["I12", ""], + ["L12", ""], + ["L12", ""], + ["I12", ""], + ["I12", ""], + ["M12", ""], + ["K1,R10,S1", "R->K(1)S(1)"], + ["T12", ""], + ["F12", ""], + ["K12", ""], + ["F1,V11", "V->F(1)"], + ["S12", ""], + ["I12", ""], + ["W12", ""], + ["N12", ""], + ["L12", ""], + ["D12", ""], + ["Y12", ""], + ["I12", ""], + ["I11,T1", ""], + ["N12", ""], + ["L12", ""], + ["I12", ""], + ["I12", ""], + ["K12", ""], + ["N12", ""], + ["L12", ""], + ["F1,S11", "C->F(1)"], + ["K12", ""], + ["S12", ""], + ["L12", ""], + ["T12", ""], + ["E12", ""], + ["N12", ""], + ["K12", ""], + ["Y12", ""], + ["S12", ""], + ["Q12", ""], + ["L12", ""], + ["D12", ""], + ["E12", ""], + ["E12", ""], + ["Q12", ""], + ["L1,P11", "P->L(1)"], + ["M12", ""], + ["E12", ""], + ["I12", ""], + ["C1,D11", "Y->C(1)"] + ] + } + }, + "tested":{ + "0":{ + "EPI_ISL_1181694_HCOV_19_USA_DE_DHSS_B1064373_2021":"test", + "EPI_ISL_1284652_HCOV_19_GERMANY_SN_RKI_I_038291_2021":"test", + "EPI_ISL_1442952_HCOV_19_SINGAPORE_321_2021":"test", + "EPI_ISL_1470937_HCOV_19_USA_NY_PRL_2021_03_29_01C17_2021":"test", + "EPI_ISL_1512225_HCOV_19_USA_GA_CDC_STM_000041012_2021":"test", + "EPI_ISL_1516887_HCOV_19_AUSTRALIA_QLD1826_2021":"test", + "EPI_ISL_1533793_HCOV_19_INDIA_MH_NCCS_CHN21027888_2021":"test", + "EPI_ISL_1533799_HCOV_19_INDIA_MH_NCCS_9947_2021":"test", + "EPI_ISL_1543980_HCOV_19_SINGAPORE_490_2021":"test", + 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"timer":5 + }, + "Residue N analysis":{ + "order":21, + "timer":5 + }, + "Residue P analysis":{ + "order":21, + "timer":5 + }, + "Residue Q analysis":{ + "order":21, + "timer":5 + }, + "Residue R analysis":{ + "order":21, + "timer":6 + }, + "Residue S analysis":{ + "order":21, + "timer":5 + }, + "Residue T analysis":{ + "order":21, + "timer":5 + }, + "Residue V analysis":{ + "order":21, + "timer":5 + }, + "Residue W analysis":{ + "order":21, + "timer":5 + }, + "Residue Y analysis":{ + "order":21, + "timer":5 + } + } +} \ No newline at end of file diff -r 5e8d0e777033 -r 60eec78ee26f test-data/summary/ORF6.MEME-full.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/ORF6.MEME-full.json Wed Jun 09 07:00:42 2021 +0000 @@ -0,0 +1,2444 @@ +{ + "MLE":{ + "content":{ + "0": [ +[235.7472979068722, 0, 1, 0.9943760343206508, 0, 0, 0.6666666666666666, 0, 0, -31.93549672470295, -31.93549672470295], + [3.125033384621221, 0, 1, 6.6249901946859, 0, 0, 0.6666666666666666, 0, 0, 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0.4459123814638887, 0, 0, -66.77406875364495, -66.77540343038319] + ] + }, + "headers": [ +["alpha;", "Synonymous substitution rate at a site"], + ["β-", "Non-synonymous substitution rate at a site for the negative/neutral evolution component"], + ["p-", "Mixture distribution weight allocated to β-; loosely -- the proportion of the tree evolving neutrally or under negative selection"], + ["β+", "Non-synonymous substitution rate at a site for the positive/neutral evolution component"], + ["p+", "Mixture distribution weight allocated to β+; loosely -- the proportion of the tree evolving neutrally or under positive selection"], + ["LRT", "Likelihood ratio test statistic for episodic diversification, i.e., p+ > 0 and β+ > α"], + ["p-value", "Asymptotic p-value for episodic diversification, i.e., p+ > 0 and β+ > α"], + ["# branches under selection", "The (very approximate and rough) estimate of how many branches may have been under selection at this site, i.e., had an empirical Bayes factor of 100 or more for the β+ rate"], + ["Total branch length", "The total length of branches contributing to inference at this site, and used to scale dN-dS"], + ["MEME LogL", "Site Log-likelihood under the MEME model"], + ["FEL LogL", "Site Log-likelihood under the FEL model"] + ] + }, + "analysis":{ + "authors":"Sergei L. Kosakovsky Pond, Steven Weaver", + "citation":"Detecting Individual Sites Subject to Episodic Diversifying Selection. _PLoS Genet_ 8(7): e1002764.", + "contact":"spond@temple.edu", + "info":"MEME (Mixed Effects Model of Evolution)\n estimates a site-wise synonymous (α) and a two-category mixture of non-synonymous\n (β-, with proportion p-, and β+ with proportion [1-p-]) rates, and\n uses a likelihood ratio test to determine if β+ > α at a site.\n The estimates aggregate information over a proportion of branches at a site,\n so the signal is derived from\n episodic diversification, which is a combination of strength of selection [effect size] and\n the proportion of the tree affected. A subset of branches can be selected\n for testing as well, in which case an additional (nuisance) parameter will be\n inferred -- the non-synonymous rate on branches NOT selected for testing. Multiple partitions within a NEXUS file are also supported\n for recombination - aware analysis.\n ", + "requirements":"in-frame codon alignment and a phylogenetic tree", + "version":"2.1.2" + }, + "branch attributes":{ + "0":{ + "Node100":{ + "Global MG94xREV":0.005595771389995104, + "Nucleotide GTR":0.005480709230504446 + }, + "Node112":{ + "Global MG94xREV":0.005601039668885619, + "Nucleotide GTR":0.005479616709115599 + }, + "Node115":{ + "Global MG94xREV":0.005593919439547744, + "Nucleotide GTR":0.0054731375250642 + }, + "Node119":{ + "Global MG94xREV":0.00560632712449723, + "Nucleotide GTR":0.00547792745634657 + }, + "Node172":{ + "Global MG94xREV":0.005628805315829838, + "Nucleotide GTR":0.005503005696410831 + }, + "Node177":{ + "Global MG94xREV":0.005582953695602026, + "Nucleotide GTR":0.005475013711016215 + }, + "Node184":{ + "Global MG94xREV":0.005597986108256508, + "Nucleotide GTR":0.005474986566233221 + }, + "Node194":{ + "Global MG94xREV":0.005557725672243263, + "Nucleotide 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"gb_MT447156_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_THA_SI200383_NT_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0.005594417293215322, + "Nucleotide GTR":0.005477059841797375, + "original name":"gb_MT447156_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_THA_SI200383_NT_2020_Segment_null_Host_Human" + }, + "gb_MT449654_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_1063_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0, + "Nucleotide GTR":0, + "original name":"gb_MT449654_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_1063_2020_Segment_null_Host_Human" + }, + "gb_MT451104_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC203_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0, + "Nucleotide GTR":0, + "original 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"gb_MT601276_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_BCSIR_NILMRC_52_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0.005591410289624195, + "Nucleotide GTR":0.005472320917083399, + "original name":"gb_MT601276_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_BCSIR_NILMRC_52_2020_Segment_null_Host_Human" + }, + "gb_MT601281_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_BCSIR_NILMRC_67_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0.005699222841336904, + "Nucleotide GTR":0.005541174876424373, + "original name":"gb_MT601281_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_BCSIR_NILMRC_67_2020_Segment_null_Host_Human" + }, + "gb_MT612186_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC1576_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0.005585829046704516, 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"gb_MT641697_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC595_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0, + "Nucleotide GTR":0, + "original name":"gb_MT641697_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC595_2020_Segment_null_Host_Human" + }, + "gb_MT683417_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_UW_10131_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0.005593469729805412, + "Nucleotide GTR":0.005474004634873228, + "original name":"gb_MT683417_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_UW_10131_2020_Segment_null_Host_Human" + }, + "gb_MT706153_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_UW_32_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0.005577547296049738, + "Nucleotide GTR":0.005469223246210523, + "original 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"gb_MT750335_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_1794_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0.005624635325623979, + "Nucleotide GTR":0.005504845328896214, + "original name":"gb_MT750335_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_1794_2020_Segment_null_Host_Human" + }, + "gb_MT772447_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_IL_UW_670_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0.005606808725804134, + "Nucleotide GTR":0.005476520487977195, + "original name":"gb_MT772447_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_IL_UW_670_2020_Segment_null_Host_Human" + }, + "gb_MT782360_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_04172_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0, + "Nucleotide GTR":0, + "original 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"gb_MW490946_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_BPHL_2353_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0, + "Nucleotide GTR":0, + "original name":"gb_MW490946_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_BPHL_2353_2020_Segment_null_Host_Human" + }, + "gb_MW491211_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_BPHL_2755_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0.005571456515223237, + "Nucleotide GTR":0.005473534846643134, + "original name":"gb_MW491211_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_BPHL_2755_2020_Segment_null_Host_Human" + }, + "gb_MW493999_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_S3367_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0.005599041993646883, + "Nucleotide GTR":0.005479467003492122, + "original name":"gb_MW493999_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_S3367_2020_Segment_null_Host_Human" + }, + "gb_MW494387_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_NH_CDC_STM_A100009_2021_Segment_null_Host_Human":{ + "Global MG94xREV":0.005639680120219169, + "Nucleotide GTR":0.005526708482947178, + "original name":"gb_MW494387_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_NH_CDC_STM_A100009_2021_Segment_null_Host_Human" + }, + "gb_MW505295_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_TX_QDX_3142_2021_Segment_null_Host_Human":{ + "Global MG94xREV":0, + "Nucleotide GTR":0, + "original name":"gb_MW505295_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_TX_QDX_3142_2021_Segment_null_Host_Human" + }, + "gb_MW509810_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_EGY_CUNCI_HGC11I035_2021_Segment_null_Host_Human":{ + "Global MG94xREV":0.005586088008998721, + "Nucleotide GTR":0.005465473449096384, + "original name":"gb_MW509810_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_EGY_CUNCI_HGC11I035_2021_Segment_null_Host_Human" + }, + "gb_MW518151_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_IN_CDC_STM_A008_2021_Segment_null_Host_Human":{ + "Global MG94xREV":0.005634240631758829, + "Nucleotide GTR":0.005500779085909651, + "original name":"gb_MW518151_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_IN_CDC_STM_A008_2021_Segment_null_Host_Human" + }, + "gb_MW519641_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CT_CDC_STM_A100453_2021_Segment_null_Host_Human":{ + "Global 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"gb_MW523039_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_GA_GPHL_0001_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0.005587898066365767, + "Nucleotide GTR":0.005470868608525645, + "original name":"gb_MW523039_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_GA_GPHL_0001_2020_Segment_null_Host_Human" + }, + "gb_MW524907_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_RI_CDC_STM_0000013_C05_2021_Segment_null_Host_Human":{ + "Global MG94xREV":0.005599551475806311, + "Nucleotide GTR":0.005472272589954402, + "original name":"gb_MW524907_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_RI_CDC_STM_0000013_C05_2021_Segment_null_Host_Human" + }, + "gb_MW528771_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_QDX_3759_2021_Segment_null_Host_Human":{ + "Global 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"gb_MW543039_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_AZ_CDC_IR9K_5198_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0, + "Nucleotide GTR":0, + "original name":"gb_MW543039_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_AZ_CDC_IR9K_5198_2020_Segment_null_Host_Human" + }, + "gb_MW545207_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_QDX_3609_2021_Segment_null_Host_Human":{ + "Global MG94xREV":0.005624669920591335, + "Nucleotide GTR":0.005504879338741244, + "original name":"gb_MW545207_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_QDX_3609_2021_Segment_null_Host_Human" + }, + "gb_MW545248_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_QDX_3654_2021_Segment_null_Host_Human":{ + "Global MG94xREV":0.005607827458873945, + "Nucleotide 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}, + "gb_MW549223_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_S3727_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0.005610072814509211, + "Nucleotide GTR":0.005484688677972459, + "original name":"gb_MW549223_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_S3727_2020_Segment_null_Host_Human" + }, + "gb_MW549830_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2465_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0, + "Nucleotide GTR":0, + "original name":"gb_MW549830_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2465_2020_Segment_null_Host_Human" + }, + "gb_MW549937_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_QDX_3900_2021_Segment_null_Host_Human":{ + "Global MG94xREV":0, + "Nucleotide GTR":0, + "original name":"gb_MW549937_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_QDX_3900_2021_Segment_null_Host_Human" + }, + "gb_MW550020_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_ME_QDX_3871_2021_Segment_null_Host_Human":{ + "Global MG94xREV":0.005594324521607599, + "Nucleotide GTR":0.005473534074566229, + "original name":"gb_MW550020_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_ME_QDX_3871_2021_Segment_null_Host_Human" + }, + "gb_MW550118_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_QDX_4040_2021_Segment_null_Host_Human":{ + "Global MG94xREV":0.005569435803716104, + "Nucleotide GTR":0.005469423349423537, + "original name":"gb_MW550118_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_QDX_4040_2021_Segment_null_Host_Human" + }, + "gb_MW550458_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WY_CDC_2_3767594_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0.005594393610046846, + "Nucleotide GTR":0.005471472344810627, + "original name":"gb_MW550458_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WY_CDC_2_3767594_2020_Segment_null_Host_Human" + }, + "gb_MW550504_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_CDC_2_3768672_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0.005606730226665676, + "Nucleotide GTR":0.005481420688897495, + "original name":"gb_MW550504_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_CDC_2_3768672_2020_Segment_null_Host_Human" + }, + "gb_MW550636_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_PA_CDC_2_3768676_2020_Segment_null_Host_Human":{ + "Global 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"gb_MW560924_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_LACPHL_AF00280_2021_Segment_null_Host_Human":{ + "Global MG94xREV":0.02284509533431139, + "Nucleotide GTR":0.02236069034936522, + "original name":"gb_MW560924_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_LACPHL_AF00280_2021_Segment_null_Host_Human" + }, + "gb_MW564865_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_14906_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0.005594417446316588, + "Nucleotide GTR":0.005477059988349209, + "original name":"gb_MW564865_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_14906_2020_Segment_null_Host_Human" + }, + "gb_MW564882_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_14886_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0, + "Nucleotide GTR":0, + "original name":"gb_MW564882_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_14886_2020_Segment_null_Host_Human" + }, + "gb_MW565403_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_14413_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0.005628420377808867, + "Nucleotide GTR":0.00550395192954325, + "original name":"gb_MW565403_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_14413_2020_Segment_null_Host_Human" + }, + "gb_MW565438_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_14344_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0, + "Nucleotide GTR":0, + "original name":"gb_MW565438_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_14344_2020_Segment_null_Host_Human" + }, + "gb_MW565832_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0724_2021_Segment_null_Host_Human":{ + "Global MG94xREV":0.005637930624046485, + "Nucleotide GTR":0.005504055374831891, + "original name":"gb_MW565832_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0724_2021_Segment_null_Host_Human" + }, + "gb_MW566477_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_QDX_4490_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0, + "Nucleotide GTR":0, + "original name":"gb_MW566477_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_QDX_4490_2020_Segment_null_Host_Human" + }, + "gb_MW566557_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_TX_QDX_4471_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0.005644974643171127, + "Nucleotide GTR":0.005507465784741251, + "original name":"gb_MW566557_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_TX_QDX_4471_2020_Segment_null_Host_Human" + }, + "gb_MW566849_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_BPHL_2886_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0.005597894897064459, + "Nucleotide GTR":0.00547573581121221, + "original name":"gb_MW566849_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_BPHL_2886_2020_Segment_null_Host_Human" + }, + "gb_MW566943_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_BPHL_2980_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0.005594439109235765, + "Nucleotide GTR":0.005477082299501769, + "original name":"gb_MW566943_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_BPHL_2980_2020_Segment_null_Host_Human" + }, + "gb_MW571108_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_GHA_WACCBIP_nCoV_GS49_2021_Segment_null_Host_Human":{ + "Global MG94xREV":0.00561060721171603, + "Nucleotide GTR":0.005482620664733259, + "original name":"gb_MW571108_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_GHA_WACCBIP_nCoV_GS49_2021_Segment_null_Host_Human" + }, + "gb_MW571118_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_GHA_WACCBIP_nCoV_GS145_2021_Segment_null_Host_Human":{ + "Global MG94xREV":0.00564497413082662, + "Nucleotide GTR":0.005507465284314313, + "original name":"gb_MW571118_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_GHA_WACCBIP_nCoV_GS145_2021_Segment_null_Host_Human" + }, + "gb_MW571185_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_GHA_WACCBIP_nCoV_GS69_2021_Segment_null_Host_Human":{ + "Global 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"gb_MW585898_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_CDC_STM_000003612_2021_Segment_null_Host_Human":{ + "Global MG94xREV":0.005601622409671225, + "Nucleotide GTR":0.005469327603117374, + "original name":"gb_MW585898_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_CDC_STM_000003612_2021_Segment_null_Host_Human" + }, + "gb_MW586184_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_CDC_STM_000005891_2021_Segment_null_Host_Human":{ + "Global MG94xREV":0.005602458594050764, + "Nucleotide GTR":0.005472270976472237, + "original name":"gb_MW586184_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_CDC_STM_000005891_2021_Segment_null_Host_Human" + }, + "gb_MW586256_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_CDC_STM_000005477_2021_Segment_null_Host_Human":{ + "Global MG94xREV":0.005624783848606779, + "Nucleotide GTR":0.005540564899378007, + "original name":"gb_MW586256_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_CDC_STM_000005477_2021_Segment_null_Host_Human" + }, + "gb_MW586274_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_TX_CDC_STM_000005611_2021_Segment_null_Host_Human":{ + "Global MG94xREV":0.005600641474542659, + "Nucleotide GTR":0.005470495330964893, + "original name":"gb_MW586274_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_TX_CDC_STM_000005611_2021_Segment_null_Host_Human" + }, + "gb_MW586385_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_LA_CDC_STM_000005076_2021_Segment_null_Host_Human":{ + "Global MG94xREV":0.00559959639929567, + "Nucleotide GTR":0.005469223246210523, + "original 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nucleotide A to nucleotide C":0.4395430104915295, + "Substitution rate from nucleotide A to nucleotide G":1, + "Substitution rate from nucleotide A to nucleotide T":0.1216209022619113, + "Substitution rate from nucleotide C to nucleotide G":0.1952279380624755, + "Substitution rate from nucleotide C to nucleotide T":1.466497674587222, + "Substitution rate from nucleotide G to nucleotide T":0.7918204256778225 + }, + "display order":0, + "estimated parameters":359 + } + }, + "input":{ + "file name":"/home/aglucaci/SARS-CoV-2/clades/B-1-617/ORF6.combined.fas", + "number of sequences":177, + "number of sites":61, + "partition count":1, + "trees":{ + 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contributing to inference at this site, and used to scale dN-dS"] + ] + }, + "analysis":{ + "authors":"Sergei L Kosakovsky Pond and Simon DW Frost", + "citation":"Not So Different After All: A Comparison of Methods for Detecting Amino Acid Sites Under Selection (2005). _Mol Biol Evol_ 22 (5): 1208-1222", + "contact":"spond@temple.edu", + "info":"SLAC (Single Likelihood Ancestor Counting)\n uses a maximum likelihood ancestral state reconstruction\n and minimum path substitution counting to estimate site - level\n dS and dN,\n and applies a simple binomial - based test to test\n if dS differs drom dN.\n The estimates aggregate information over all branches,\n so the signal is derived from\n pervasive diversification or conservation. A subset of branches can be selected\n for testing as well.\n Multiple partitions within a NEXUS file are also supported\n for recombination - aware analysis.\n ", + "requirements":"in-frame codon alignment and a phylogenetic tree", + "version":"2.00" + }, + "branch attributes":{ + "0":{ + "Node100":{ + "Global MG94xREV":0.005590443923023665, + "Nucleotide GTR":0.005480709230504446, + "amino-acid": [ +["M", "F", "H", "R", "V", "D", "F", "Q", "V", "T", "I", "A", "E", "I", "L", "L", "I", "I", "M", "R", "T", "F", "K", "V", "S", "I", "W", "N", "L", "D", "Y", "I", "I", "N", "L", "I", "I", "K", "N", "L", "S", "K", "S", "L", "T", "E", "N", "K", "Y", "S", "Q", "L", "D", "E", "E", "Q", "P", "M", "E", "I", "D"] + ], + "codon": [ +["ATG", "TTT", "CAT", "CGC", "GTT", "GAC", "TTT", "CAG", "GTT", "ACT", "ATA", "GCA", "GAG", "ATA", "TTA", "CTA", "ATT", "ATT", "ATG", "AGG", "ACT", "TTT", "AAA", "GTT", "TCC", "ATT", "TGG", "AAT", "CTT", "GAT", "TAC", "ATC", "ATA", "AAC", "CTC", "ATA", "ATT", "AAA", 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"gb_MW586274_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_TX_CDC_STM_000005611_2021_Segment_null_Host_Human":"test", + "gb_MW586385_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_LA_CDC_STM_000005076_2021_Segment_null_Host_Human":"test", + "gb_MW586419_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_IA_CDC_STM_000005050_2021_Segment_null_Host_Human":"test", + "gb_MW586670_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_CDC_STM_000003618_2021_Segment_null_Host_Human":"test", + "gb_MW586700_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_QDX_4173_2021_Segment_null_Host_Human":"test", + "gb_MW586846_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_NY_QDX_4256_2021_Segment_null_Host_Human":"test", + "gb_MW586849_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_PA_QDX_4292_2021_Segment_null_Host_Human":"test", + "gb_MW592637_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01774_2021_Segment_null_Host_Human":"test", + "gb_MW592782_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2311_2020_Segment_null_Host_Human":"test", + "gb_MW593179_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FHCRC_1171_2020_Segment_null_Host_Human":"test", + "gb_MW593378_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FHCRC_8518_2020_Segment_null_Host_Human":"test", + "gb_MW593611_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FHCRC_7938_2020_Segment_null_Host_Human":"test", + "gb_MW593708_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FHCRC_4325_2020_Segment_null_Host_Human":"test", + "gb_MW596234_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_LA_CDC_STM_000008248_2021_Segment_null_Host_Human":"test", + "gb_MW598427_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_GHA_nmimr_SARS_CoV_2_NTRA_15010_2020_Segment_null_Host_Human":"test", + "gb_MW599514_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_Broad_CRSP_00376_2021_Segment_null_Host_Human":"test", + "gb_MW599662_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_RI_Broad_RIDOH_00108_2020_Segment_null_Host_Human":"test" + } + }, + "timers":{ + "Model fitting":{ + "order":1, + "timer":3 + }, + "Primary SLAC analysis":{ + "order":2, + "timer":1 + }, + "Total time":{ + "order":0, + "timer":4 + } + } +} \ No newline at end of file diff -r 5e8d0e777033 -r 60eec78ee26f test-data/summary/ORF6.combined.fas --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/ORF6.combined.fas Wed Jun 09 07:00:42 2021 +0000 @@ -0,0 +1,531 @@ +>epi_isl_1181694/hCoV-19/USA/DE-DHSS-B1064373/2021 +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>epi_isl_1284652/hCoV-19/Germany/SN-RKI-I-038291/2021 +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCACAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>epi_isl_1442952/hCoV-19/Singapore/321/2021 +ATGTTTCATCTCGTTGGCTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>epi_isl_1512225/hCoV-19/USA/GA-CDC-STM-000041012/2021 +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGTACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>epi_isl_1470937/hCoV-19/USA/NY-PRL-2021_03_29_01C17/2021 +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAC + +>epi_isl_1516887/hCoV-19/Australia/QLD1826/2021 +ATGTTTCATCTCGTTGACTTTCATGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>epi_isl_1533793/hCoV-19/India/MH-NCCS-CHN21027888/2021 +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATCTGT + +>epi_isl_1533799/hCoV-19/India/MH-NCCS-9947/2021 +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATACTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>epi_isl_1543980/hCoV-19/Singapore/490/2021 +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATTTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>epi_isl_1589923/hCoV-19/India/WB-1930300571091/2021 +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAAGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>epi_isl_1589926/hCoV-19/India/WB-1930300586246/2021 +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAATTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>epi_isl_1631286/hCoV-19/England/CAMC-14E7527/2021 +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACTAATGGAGATTGAT + + +>REFERENCE +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW593708_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FHCRC_4325_2020_Segment_null_Host_Human +AGATGTTATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MT860680_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_DNAS_DRICM_isl_MH_09_2020_Segment_null_Host_Human 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+>gb_MW550458_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WY_CDC_2_3767594_2020_Segment_null_Host_Human +ATGTTCCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW564865_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_14906_2020_Segment_null_Host_Human +ATGTTTCACCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MT890240_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_GHA_2709_S25_2020_Segment_null_Host_Human +ATGTTTCATATCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MT811295_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_SEARCH_0657_IPL_2020_Segment_null_Host_Human +ATGTTTCATCACGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MT811511_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_SEARCH_1079_SAN_2020_Segment_null_Host_Human +ATGTTTCATCCCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW564882_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_14886_2020_Segment_null_Host_Human 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+ATGTTTCATCTCGTTAACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW243997_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0302_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACCTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW265628_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_201129040_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTCTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW566477_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_QDX_4490_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTCTCAGGTTACTATAGCAGAGATGTTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MT627613_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_S260_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTCCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAC + +>gb_MT940472_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_IND_GBRC334a_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTCCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW593611_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FHCRC_7938_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTAACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW599514_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_Broad_CRSP_00376_2021_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACCATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MT601276_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_BCSIR_NILMRC_52_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTACAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW519641_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CT_CDC_STM_A100453_2021_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGACATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW524907_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_RI_CDC_STM_0000013_C05_2021_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATCACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW583187_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_OK_CDC_STM_000003021_2021_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATAATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MT782360_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_04172_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATCATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW467498_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_EGY_EGY_CCHE57357_P_32_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGAACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW571118_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_GHA_WACCBIP_nCoV_GS145_2021_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGAATTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW452545_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_TUN_TUN_ADAGE_T_15425_20_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACCTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW545207_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_QDX_3609_2021_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATTGAGATTGAT + +>gb_MW375980_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_201216229_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTC---------------------------ATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MT358638_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_DEU_FFM1_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGCTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW528794_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_QDX_3784_2021_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCAATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW550504_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_CDC_2_3768672_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATGTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW208032_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_VA_DCLS_1590_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTAGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW056168_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_BPHL_1521_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTCGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MT447156_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_THA_SI200383_NT_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAACCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MT825091_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_IRN_COVID19_IRVSH1_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTAGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW550636_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_PA_CDC_2_3768676_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTAATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW545306_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_QDX_3723_2021_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGAC---ATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW490888_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_BPHL_2295_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATCACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW134227_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_3762_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACACCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW490862_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_BPHL_2441_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCACGAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW341989_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_UW_2124_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAAACTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW155642_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC13394_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCGCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW406537_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_IN_CDC_2_3693679_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCACAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MT683417_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_UW_10131_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAACTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW566943_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_BPHL_2980_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATCAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MT631787_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_1651_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAAATTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW486406_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_UW_2638_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATCTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW592782_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2311_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTCAACCAATGGAGATTG------------------------------------------------ + +>gb_MW157056_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC11469_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTACCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MT811669_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_SEARCH_0155_NBG_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTAGCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW566557_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_TX_QDX_4471_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAAATGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW181739_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_Homo_sapiens_HKG_Case5119_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACGGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW549223_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_S3727_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAAAAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW549937_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_QDX_3900_2021_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAACAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW598427_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_GHA_nmimr_SARS_CoV_2_NTRA_15010_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAACATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW295643_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_TUN_TUN_202058412_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCCCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MT834049_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_S1626_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCGCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW586184_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_CDC_STM_000005891_2021_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAACTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW467476_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_EGY_EGY_CCHE57357_A_71_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAAATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW462661_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2263_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGACGAAGAGCAACCAATGGAGATTGAT + +>gb_MW433771_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_LACPHL_AF00076_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATAAAGAGCAACCAATGGAGATTGAT + +>gb_MT612186_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC1576_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAACGGAGATTGAT + +>gb_MW035934_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_2214_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGACTGAT + +>gb_MT520188_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MGH_00184_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTAAA + +>gb_MW586700_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_QDX_4173_2021_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTAAT + +>gb_MW156645_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC11076_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTCAT + +>gb_MW156840_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC11409_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTCTC + +>gb_MW332559_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BHR_341036734_S5_L001_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAA + +>gb_MW523039_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_GA_GPHL_0001_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGGT + +>gb_MW156971_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC10203_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTTAT + +>gb_MT946870_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_S2716_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGCTTGAT + +>gb_MW532096_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_GRBL_S4_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGGTTGAT + +>gb_MW586849_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_PA_QDX_4292_2021_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGATATTGAT + +>gb_MW528771_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_QDX_3759_2021_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGGGATTGAT + +>gb_MW593378_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FHCRC_8518_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCATTGGAGATTGAT + +>gb_MW064863_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_QDX_779_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCTATGGAGATTGAT + +>gb_MW321239_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC17424_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAGCCAATGGAGATTGAT + +>gb_MW592637_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01774_2021_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCTACCAATGGAGATTGAT + +>gb_MW134116_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_3258_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGATCAACCAATGGAGATTGAT + +>gb_MW190571_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_QDX_1809_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAGGAGCAACCAATGGAGATTGAT + +>gb_MT449654_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_1063_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGGTGAAGAGCAACCAATGGAGATTGAT + +>gb_MW093451_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_TX_DSHS_0533_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGTTGAAGAGCAACCAATGGAGATTGAT + +>gb_MT745697_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC2124_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTATATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW047313_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WRCEVA_000509_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTGGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW586419_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_IA_CDC_STM_000005050_2021_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAGTTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW586256_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_CDC_STM_000005477_2021_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCTATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW518151_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_IN_CDC_STM_A008_2021_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTTTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MT641697_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC595_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATGTTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW491211_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_BPHL_2755_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATTTTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW596234_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_LA_CDC_STM_000008248_2021_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAACTATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW509810_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_EGY_CUNCI_HGC11I035_2021_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAATTATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MT772447_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_IL_UW_670_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATGAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW064840_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MI_QDX_825_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGACTAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW155738_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC11358_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAGTAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MT706153_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_UW_32_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGGGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW555931_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_S3980_2021_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAATTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW556173_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_IL_CDC_9MPQ_8899_2021_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAGCTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MT326182_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CT_UW_1365_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTTACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW447630_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_PAK_JRCGR_KHI15_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCAGTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MT520493_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MGH_00316_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCATTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW583265_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_000001669_2021_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAATTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW565832_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0724_2021_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATGTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW519702_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_IN_CDC_STM_A100466_2021_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTGTCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW519849_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_PA_CDC_STM_A100104_2021_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAGTTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MT601281_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_BCSIR_NILMRC_67_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAATATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW549830_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2465_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAGAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW565438_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_14344_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCGTAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW550020_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_ME_QDX_3871_2021_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCTTAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW553298_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_ARG_Cordoba_1006_155_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACTTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MT359866_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_ESP_VH198152683_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAGCCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW155761_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC10624_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATTATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW566849_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_BPHL_2886_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACGTCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW547503_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_EGY_CUNCI_HGC09I039_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTATATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW154346_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC7465_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTGCATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW565403_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_14413_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTTATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW206535_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_BPHL_1865_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATGTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW585898_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_CDC_STM_000003612_2021_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGGATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MT873189_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_DPH_00301_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGTAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW483548_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_13407_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTTGAATCTTGATTACACCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MT973414_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_TAS83_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTTGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW494387_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_NH_CDC_STM_A100009_2021_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTTGAATCTTGATTACATTATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW155278_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC12385_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCGTTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW181508_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_201017695_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCGATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW593179_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FHCRC_1171_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCTATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAC + +>gb_MW474247_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_S3080_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCTATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MT847221_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_BCSIR_NILMRC_283_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTTCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW321253_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC17363_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGATTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW539842_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_00583_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGATGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW493999_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_S3367_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGCGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW545248_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_QDX_3654_2021_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATTAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW578246_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0808_2021_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATTAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAGAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW578233_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0795_2021_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTGTGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW505295_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_TX_QDX_3142_2021_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTGTTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW543039_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_AZ_CDC_IR9K_5198_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTACTTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW244002_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0307_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTATTTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW543030_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_AZ_CDC_IR9A_6594_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTATTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW490743_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_BPHL_2463_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTGCTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW599662_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_RI_Broad_RIDOH_00108_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATGTTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW586385_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_LA_CDC_STM_000005076_2021_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGGTATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MT913013_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_DNAS_DRICM_isl_Sharmin_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGATATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MT969697_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC2890_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGTGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW490946_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_BPHL_2353_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCGGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW277035_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC16243_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCTGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW586670_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_CDC_STM_000003618_2021_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGTAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MT750335_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_1794_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCAGTTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW181734_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_Homo_sapiens_HKG_Case5054_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCCGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW550118_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_QDX_4040_2021_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTCGGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW550674_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_SC_CDC_2_3767563_2021_Segment_null_Host_Human +ATGTTTCATCTCGTTGACTTTGAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MT940460_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_IND_GBRC331_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTGATTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MT451104_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC203_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTTACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW521749_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_NV_QDX_3543_2020_Segment_null_Host_Human +ATGTTTCATCTCGTTTACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTATATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_LC571023_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_DP0724_Segment_null_Host_Human +ATGTTTCATCTCTTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW586846_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_NY_QDX_4256_2021_Segment_null_Host_Human +ATGTTTCATCTTGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATCCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT + +>gb_MW571185_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_GHA_WACCBIP_nCoV_GS69_2021_Segment_null_Host_Human +ATGTTTCATCTTGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTCTC + +>gb_MT745746_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_SA01_2020_Segment_null_Host_Human 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"gb_MW599514_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_Broad_CRSP_00376_2021_Segment_null_Host_Human":"Reference", + "gb_MW599662_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_RI_Broad_RIDOH_00108_2020_Segment_null_Host_Human":"Reference" +} \ No newline at end of file diff -r 5e8d0e777033 -r 60eec78ee26f test-data/summary/merged-segment.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/merged-segment.json Wed Jun 09 07:00:42 2021 +0000 @@ -0,0 +1,132 @@ +{ + "nsp7": { + "map": [], + "tree": 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+ "tree_tags": {} + } +} \ No newline at end of file diff -r 5e8d0e777033 -r 60eec78ee26f test-data/summary/merged-site.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/merged-site.json Wed Jun 09 07:00:42 2021 +0000 @@ -0,0 +1,1 @@ +{} \ No newline at end of file diff -r 5e8d0e777033 -r 60eec78ee26f test-data/summary/nsp7-segment.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/nsp7-segment.json Wed Jun 09 07:00:42 2021 +0000 @@ -0,0 +1,7 @@ +{ + "nsp7": { + "map": [], + "tree": 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+ "tree_tags": {} + } +} \ No newline at end of file diff -r 5e8d0e777033 -r 60eec78ee26f test-data/summary/nsp7-site.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/nsp7-site.json Wed Jun 09 07:00:42 2021 +0000 @@ -0,0 +1,1 @@ +{} \ No newline at end of file diff -r 5e8d0e777033 -r 60eec78ee26f test-data/summary/nsp7.FADE.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/nsp7.FADE.json Wed Jun 09 07:00:42 2021 +0000 @@ -0,0 +1,3775 @@ +{ + "MLE":{ + "content":{ + "A":{ + "0": [ +[2.135355976597445, 4.42736879646139, 0.9442611618171569, 0.948440123871129], + [2.693374054144683, 5.447411670296412, 0.9467570683845876, 0.9955252951947779], + [1.688653150925858, 5.451721466912741, 0.9466016845428151, 0.9924655022317769], + [2.135355976597445, 4.42736879646139, 0.9442611618171569, 0.948440123871129], + [1.895030664619211, 4.52086406954309, 0.9445058895733424, 0.9528696179522672], + [1.758305195386422, 3.944714326314311, 0.9429120087101439, 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rate at a site"], + ["bias", "Mean posterior bias parameter at a site"], + ["Prob[bias>0]", "Posterior probability of substitution bias"], + ["BayesFactor[bias>0]", "Empiricial Bayes Factor for substitution bias"] + ] + }, + "analysis":{ + "authors":"Sergei L Kosakovsky Pond", + "citation":"TBD", + "contact":"spond@temple.edu", + "info":"FADE (FUBAR Approach to Directional Evolution) is a fast method to test whether or not a subset of sites in a protein alignment\n evolve towards a particular residue along a subset of branches at accelerated rates compared to reference model.\n FADE uses a random effects model and latent Dirichlet allocation (LDA) - inspired approximation methods to allocate sites to rate classes.", + "requirements":"A protein alignment and a **rooted** phylogenetic tree (optionally annotated with {})", + "version":"0.2" + }, + "branch attributes":{ + "0":{ + "EPI_ISL_1181694_HCOV_19_USA_DE_DHSS_B1064373_2021":{ + "GTR":0, + "original 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loosely -- the proportion of the tree evolving neutrally or under negative selection"], + ["β+", "Non-synonymous substitution rate at a site for the positive/neutral evolution component"], + ["p+", "Mixture distribution weight allocated to β+; loosely -- the proportion of the tree evolving neutrally or under positive selection"], + ["LRT", "Likelihood ratio test statistic for episodic diversification, i.e., p+ > 0 and β+ > α"], + ["p-value", "Asymptotic p-value for episodic diversification, i.e., p+ > 0 and β+ > α"], + ["# branches under selection", "The (very approximate and rough) estimate of how many branches may have been under selection at this site, i.e., had an empirical Bayes factor of 100 or more for the β+ rate"], + ["Total branch length", "The total length of branches contributing to inference at this site, and used to scale dN-dS"], + ["MEME LogL", "Site Log-likelihood under the MEME model"], + ["FEL LogL", "Site Log-likelihood under the FEL model"] + ] + }, + "analysis":{ + "authors":"Sergei L. Kosakovsky Pond, Steven Weaver", + "citation":"Detecting Individual Sites Subject to Episodic Diversifying Selection. _PLoS Genet_ 8(7): e1002764.", + "contact":"spond@temple.edu", + "info":"MEME (Mixed Effects Model of Evolution)\n estimates a site-wise synonymous (α) and a two-category mixture of non-synonymous\n (β-, with proportion p-, and β+ with proportion [1-p-]) rates, and\n uses a likelihood ratio test to determine if β+ > α at a site.\n The estimates aggregate information over a proportion of branches at a site,\n so the signal is derived from\n episodic diversification, which is a combination of strength of selection [effect size] and\n the proportion of the tree affected. A subset of branches can be selected\n for testing as well, in which case an additional (nuisance) parameter will be\n inferred -- the non-synonymous rate on branches NOT selected for testing. Multiple partitions within a NEXUS file are also supported\n for recombination - aware analysis.\n ", + "requirements":"in-frame codon alignment and a phylogenetic tree", + "version":"2.1.2" + }, + "branch attributes":{ + "0":{ + "Node126":{ + "Global MG94xREV":0.004130961000899132, + "Nucleotide GTR":0.004026916786386125 + }, + "Node13":{ + "Global MG94xREV":0.004132150313331901, + "Nucleotide GTR":0.004028684119801425 + }, + "Node133":{ + "Global MG94xREV":0.00412189884001824, + "Nucleotide GTR":0.004022166655777783 + }, + "Node154":{ + "Global MG94xREV":0.004132772796260646, + "Nucleotide GTR":0.004028684124701925 + }, + "Node160":{ + "Global MG94xREV":0.004126386634956676, + "Nucleotide GTR":0.004026548853976075 + }, + "Node166":{ + "Global MG94xREV":0.004132586115707147, + "Nucleotide GTR":0.004027901251047813 + }, + "Node17":{ + "Global MG94xREV":0.004132448425320532, + "Nucleotide GTR":0.004030919372587651 + }, + "Node171":{ + "Global MG94xREV":0.008307048312653668, + 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"original name":"gb_MT226610_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_CHN_KMS1_2020_Segment_null_Host_Human" + }, + "gb_MT291831_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_CHN_Beijing_IME_BJ01_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0.004134438198709842, + "Nucleotide GTR":0.004030916209390761, + "original name":"gb_MT291831_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_CHN_Beijing_IME_BJ01_2020_Segment_null_Host_Human" + }, + "gb_MT380729_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_VI_CDC_1999_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0.004122988137469055, + "Nucleotide GTR":0.004021304657838435, + "original name":"gb_MT380729_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_VI_CDC_1999_2020_Segment_null_Host_Human" + }, + "gb_MT412283_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CT_UW_5772_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0, + "Nucleotide GTR":0, + "original name":"gb_MT412283_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CT_UW_5772_2020_Segment_null_Host_Human" + }, + "gb_MT446348_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_LA_BIE_080_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0, + "Nucleotide GTR":0, + "original name":"gb_MT446348_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_LA_BIE_080_2020_Segment_null_Host_Human" + }, + "gb_MT451046_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC142_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0, + "Nucleotide GTR":0, + "original 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"gb_MT460125_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_1105_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0.004123357819357554, + "Nucleotide GTR":0.004022046124083386, + "original name":"gb_MT460125_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_1105_2020_Segment_null_Host_Human" + }, + "gb_MT470179_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_France_40002VJ_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0.004140616949073272, + "Nucleotide GTR":0.004028143704669125, + "original name":"gb_MT470179_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_France_40002VJ_2020_Segment_null_Host_Human" + }, + "gb_MT499218_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_TUN_COV1663_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0.004109798305448772, + "Nucleotide 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"gb_MT609579_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_VA_DCLS_0349_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0.004137966591885405, + "Nucleotide GTR":0.004035888948364675, + "original name":"gb_MT609579_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_VA_DCLS_0349_2020_Segment_null_Host_Human" + }, + "gb_MT612207_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC1606_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0, + "Nucleotide GTR":0, + "original name":"gb_MT612207_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC1606_2020_Segment_null_Host_Human" + }, + "gb_MT628119_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_1404_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0.00408534350784449, + "Nucleotide GTR":0.004015073421519414, + "original 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"original name":"gb_MW495235_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_NH_QDX_3003_2021_Segment_null_Host_Human" + }, + "gb_MW505146_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_QDX_3110_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0.004136400668624945, + "Nucleotide GTR":0.004029724705093927, + "original name":"gb_MW505146_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_QDX_3110_2020_Segment_null_Host_Human" + }, + "gb_MW517337_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_SC_COVID21_0048_2021_Segment_null_Host_Human":{ + "Global MG94xREV":0.004144479684115792, + "Nucleotide GTR":0.004035059596667426, + "original name":"gb_MW517337_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_SC_COVID21_0048_2021_Segment_null_Host_Human" + }, + "gb_MW517339_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_SC_COVID21_0044_2021_Segment_null_Host_Human":{ + "Global MG94xREV":0.004128898347904866, + "Nucleotide GTR":0.004025511464500564, + "original name":"gb_MW517339_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_SC_COVID21_0044_2021_Segment_null_Host_Human" + }, + "gb_MW517346_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_SC_COVID21_0036_2021_Segment_null_Host_Human":{ + "Global MG94xREV":0.00414134954379492, + "Nucleotide GTR":0.004037659014126361, + "original name":"gb_MW517346_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_SC_COVID21_0036_2021_Segment_null_Host_Human" + }, + "gb_MW518128_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_AZ_CDC_STM_291_2021_Segment_null_Host_Human":{ + "Global 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name":"gb_MW518847_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_NC_CDC_STM_209_2020_Segment_null_Host_Human" + }, + "gb_MW519847_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_IN_CDC_STM_A100107_2021_Segment_null_Host_Human":{ + "Global MG94xREV":0.004116140330661855, + "Nucleotide GTR":0.004020036227862966, + "original name":"gb_MW519847_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_IN_CDC_STM_A100107_2021_Segment_null_Host_Human" + }, + "gb_MW521457_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_1516xF10_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0.004138552343776219, + "Nucleotide GTR":0.004028684133734021, + "original name":"gb_MW521457_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_1516xF10_2020_Segment_null_Host_Human" + }, + "gb_MW521689_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_QDX_3455_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0.004116717428861321, + "Nucleotide GTR":0.004018669473854881, + "original name":"gb_MW521689_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_QDX_3455_2020_Segment_null_Host_Human" + }, + "gb_MW523832_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_AZ_CDC_STM_A100333_2021_Segment_null_Host_Human":{ + "Global MG94xREV":0.004136391625588471, + "Nucleotide GTR":0.004029715889499887, + "original name":"gb_MW523832_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_AZ_CDC_STM_A100333_2021_Segment_null_Host_Human" + }, + "gb_MW523879_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_IL_CDC_STM_A100264_2021_Segment_null_Host_Human":{ + "Global MG94xREV":0, + "Nucleotide GTR":0, + "original name":"gb_MW523879_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_IL_CDC_STM_A100264_2021_Segment_null_Host_Human" + }, + "gb_MW524933_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_0000014_D07_2021_Segment_null_Host_Human":{ + "Global MG94xREV":0.004129571672775585, + "Nucleotide GTR":0.004030266399156784, + "original name":"gb_MW524933_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_0000014_D07_2021_Segment_null_Host_Human" + }, + "gb_MW525001_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MI_CDC_STM_0000014_B04_2021_Segment_null_Host_Human":{ + "Global MG94xREV":0.004110938672928521, + "Nucleotide GTR":0.004020618373368076, + "original 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"gb_MW539883_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_00646_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0.004144985597111592, + "Nucleotide GTR":0.004034950627229877, + "original name":"gb_MW539883_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_00646_2020_Segment_null_Host_Human" + }, + "gb_MW539888_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_00651_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0, + "Nucleotide GTR":0, + "original name":"gb_MW539888_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_00651_2020_Segment_null_Host_Human" + }, + "gb_MW543034_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_AZ_CDC_IR9E_6611_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0, + "Nucleotide GTR":0, + "original 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"gb_MW548941_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_S3648_2021_Segment_null_Host_Human":{ + "Global MG94xREV":0.004129863035794244, + "Nucleotide GTR":0.004030909613639421, + "original name":"gb_MW548941_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_S3648_2021_Segment_null_Host_Human" + }, + "gb_MW550186_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_QDX_4128_2021_Segment_null_Host_Human":{ + "Global MG94xREV":0.004120431723760399, + "Nucleotide GTR":0.004023265820676617, + "original name":"gb_MW550186_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_QDX_4128_2021_Segment_null_Host_Human" + }, + "gb_MW550562_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_DC_CDC_2_3773950_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0.004123953471922002, + "Nucleotide GTR":0.004028273006727388, + "original name":"gb_MW550562_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_DC_CDC_2_3773950_2020_Segment_null_Host_Human" + }, + "gb_MW550565_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_CDC_2_3768593_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0.004127311416812781, + "Nucleotide GTR":0.004030954103902182, + "original name":"gb_MW550565_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_CDC_2_3768593_2020_Segment_null_Host_Human" + }, + "gb_MW550677_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_NJ_CDC_2_3768077_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0.004110958807250278, + "Nucleotide GTR":0.004018099428346693, + "original 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Host_Human,gb_MW518847_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_NC_CDC_STM_209_2020_Segment_null_Host_Human,gb_MW578033_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2101679988_2020_Segment_null_Host_Human,gb_MW306408_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_12385_2020_Segment_null_Host_Human,gb_MW064614_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MI_QDX_560_2020_Segment_null_Host_Human,(gb_MW332236_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_RUS_2272_2020_Segment_null_Host_Human,gb_MW494399_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_BPHL_2779_2021_Segment_null_Host_Human)Node126,gb_MW277234_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC15990_2020_Segment_null_Host_Human,gb_MW596017_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_CDC_STM_000007226_2021_Segment_null_Host_Human,gb_MW281864_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_West_Bank_Jericho_SARS_CoV_2_2020_Segment_null_Host_Human,gb_MW134122_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_3285_2020_Segment_null_Host_Human,gb_MW565664_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_13917_2020_Segment_null_Host_Human,gb_MW483597_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_13466_2020_Segment_null_Host_Human,epi_isl_1652109_hCoV_19_Singapore_565_2021,gb_MW524933_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_0000014_D07_2021_Segment_null_Host_Human,gb_MW320996_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC17273_2020_Segment_null_Host_Human,(gb_MT890291_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_BPHL_0812_2020_Segment_null_Host_Human,gb_MW579030_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2101421353_2021_Segment_null_Host_Human)Node61,gb_MW525004_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_NM_CDC_STM_0000014_B01_2021_Segment_null_Host_Human,(epi_isl_1564187_hCoV_19_England_CAMC_14D5BFD_2021,(gb_MW474140_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_S2964_2020_Segment_null_Host_Human,gb_MW035496_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_UW_1327_2020_Segment_null_Host_Human,gb_MW276622_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_11799_2020_Segment_null_Host_Human)Node54,gb_MT937322_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0133_2020_Segment_null_Host_Human)Node52,gb_MW550711_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_VA_CDC_2_3767585_2020_Segment_null_Host_Human,gb_MW483436_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_12951_2020_Segment_null_Host_Human,epi_isl_1416968_hCoV_19_Guadeloupe_IPP06229_2021,gb_MT451174_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC278_2020_Segment_null_Host_Human,epi_isl_1583966_hCoV_19_England_CAMC_14D1B4C_2021,(gb_MW420606_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2012663262_2020_Segment_null_Host_Human,gb_MW156759_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC13581_2020_Segment_null_Host_Human,gb_MW486330_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_UW_2532_2020_Segment_null_Host_Human)Node76,gb_MW406612_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_OK_CDC_2_3693466_2020_Segment_null_Host_Human,gb_MT940476_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_IND_GBRC336_2020_Segment_null_Host_Human,epi_isl_1415273_hCoV_19_India_MH_NCCS_87216_2021,gb_MW559163_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2101251032_2020_Segment_null_Host_Human,gb_MT380729_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_VI_CDC_1999_2020_Segment_null_Host_Human,gb_MW321295_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC17192_2020_Segment_null_Host_Human,(gb_MW454728_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Str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non-synonymous substitutions"], + ["P[S]", "Expected proportion of synonymous sites"], + ["dS", "Inferred synonymous susbsitution rate"], + ["dN", "Inferred non-synonymous susbsitution rate"], + ["dN-dS", "Scaled by the length of the tested branches"], + ["P [dN/dS > 1]", "Binomial probability that S is no greater than the observed value, with Ps probability of success"], + ["P [dN/dS < 1]", "Binomial probability that S is no less than the observed value, with Ps probability of success"], + ["Total branch length", "The total length of branches contributing to inference at this site, and used to scale dN-dS"] + ] + }, + "analysis":{ + "authors":"Sergei L Kosakovsky Pond and Simon DW Frost", + "citation":"Not So Different After All: A Comparison of Methods for Detecting Amino Acid Sites Under Selection (2005). _Mol Biol Evol_ 22 (5): 1208-1222", + "contact":"spond@temple.edu", + "info":"SLAC (Single Likelihood Ancestor Counting)\n uses a maximum likelihood ancestral state reconstruction\n and minimum path substitution counting to estimate site - level\n dS and dN,\n and applies a simple binomial - based test to test\n if dS differs drom dN.\n The estimates aggregate information over all branches,\n so the signal is derived from\n pervasive diversification or conservation. A subset of branches can be selected\n for testing as well.\n Multiple partitions within a NEXUS file are also supported\n for recombination - aware analysis.\n ", + "requirements":"in-frame codon alignment and a phylogenetic tree", + "version":"2.00" + }, + "branch attributes":{ + "0":{ + "Node126":{ + "Global MG94xREV":0.004136417827218518, + "Nucleotide GTR":0.004026916786386125, + "amino-acid": [ +["S", "K", "M", "S", "D", "V", "K", "C", "T", "S", "V", "V", "L", "L", "S", "V", "L", "Q", "Q", "L", "R", "V", "E", "S", "S", "S", "K", "L", "W", "A", "Q", "C", "V", "Q", "L", "H", "N", "D", "I", "L", "L", "A", "K", "D", "T", "T", "E", "A", "F", "E", "K", "M", "V", "S", "L", "L", "S", "V", "L", "L", "S", "M", "Q", "C", "A", "V", "D", "I", "N", "K", "L", "C", "E", "E", "M", "L", "D", "N", "R", "A", "T", "L", "Q"] + ], + "codon": [ +["TCT", "AAA", "ATG", "TCA", "GAT", "GTA", "AAG", "TGC", "ACA", "TCA", "GTA", "GTC", "TTA", "CTC", "TCA", "GTT", "TTG", "CAA", "CAA", "CTC", "AGA", "GTA", 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GTR":{ + "AIC-c":4207.652962845961, + "Equilibrium frequencies": [ +[0.316982214572576], + [0.1955372510449963], + [0.1847799360708139], + [0.3027005983116138] + ], + "Log Likelihood":-1703.562299296798, + "Rate Distributions":{ + "Substitution rate from nucleotide A to nucleotide C":0.2854468704485844, + "Substitution rate from nucleotide A to nucleotide G":1, + "Substitution rate from nucleotide A to nucleotide T":0.009867778509707405, + "Substitution rate from nucleotide C to nucleotide G":0.02709890342210576, + "Substitution rate from nucleotide C to nucleotide T":1.655264438379606, + "Substitution rate from nucleotide G to nucleotide T":0.4850813979618184 + }, + "display order":0, + "estimated parameters":397 + } + }, + "input":{ + "file name":"/home/aglucaci/SARS-CoV-2/clades/B-1-617/nsp7.combined.fas", + "number of sequences":196, + "number of sites":83, + "partition count":1, + "trees":{ + 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"gb_MW599561_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_Broad_CRSP_00424_2021_Segment_null_Host_Human":"test" + } + }, + "timers":{ + "Model fitting":{ + "order":1, + "timer":5 + }, + "Primary SLAC analysis":{ + "order":2, + "timer":2 + }, + "Total time":{ + "order":0, + "timer":7 + } + } +} \ No newline at end of file diff -r 5e8d0e777033 -r 60eec78ee26f test-data/summary/nsp7.combined.fas --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/nsp7.combined.fas Wed Jun 09 07:00:42 2021 +0000 @@ -0,0 +1,588 @@ +>epi_isl_1181694/hCoV-19/USA/DE-DHSS-B1064373/2021 +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>epi_isl_1409773/hCoV-19/England/CAMC-141DB08/2021 +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATTCTGGACAACAGGGCAACCTTACAA + +>epi_isl_1415264/hCoV-19/India/MH-NCCS-128864/2021 +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGTTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>epi_isl_1415273/hCoV-19/India/MH-NCCS-87216/2021 +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAATAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>epi_isl_1564187/hCoV-19/England/CAMC-14D5BFD/2021 +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCTATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>epi_isl_1583966/hCoV-19/England/CAMC-14D1B4C/2021 +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATTTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>epi_isl_1641831/hCoV-19/Germany/BY-RKI-I-076082/2021 +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGACATGCTGGACAACAGGGCAACCTTACAA + +>epi_isl_1648157/hCoV-19/USA/CA-CDC-QDX23571833/2021 +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTTTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAATCTTACAA + +>epi_isl_1416968/hCoV-19/Guadeloupe/IPP06229/2021 +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGATATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>epi_isl_1635400/hCoV-19/Scotland/CAMC-14DEDB2/2021 +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGCGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>epi_isl_1652109/hCoV-19/Singapore/565/2021 +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAGTGCTGGACAACAGGGCAACCTTACAA + + +>REFERENCE +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW579030_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2101421353_2021_Segment_null_Host_Human +TCAAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MT890291_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_BPHL_0812_2020_Segment_null_Host_Human +TCCAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MT890320_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_BPHL_0841_2020_Segment_null_Host_Human +TCTAAAATATCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MT810681_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_SEARCH_1240_SAN_2020_Segment_null_Host_Human +TCTAAAATGTCAGACGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW134122_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_3285_2020_Segment_null_Host_Human +TCTAAAATGTCAGATATAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW579014_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2101155076_2021_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGCAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MT937823_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0160_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTATTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW420097_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2012061461_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCATACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MT412283_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CT_UW_5772_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCCTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MT825091_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_IRN_COVID19_IRVSH1_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTCACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW156992_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC10174_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTATCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW586766_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_QDX_4270_2021_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTCTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW406516_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_AR_CDC_2_3693765_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTGTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW562693_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2102046035_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTCTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW276613_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_11950_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTCTTCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW277234_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC15990_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTACAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW578033_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2101679988_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCACCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW130870_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_CDC_6238_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCAGCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MT834677_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_BPHL_0519_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAAGTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW320996_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC17273_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTATGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW403680_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_VA_DCLS_2414_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGACTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW277113_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC12012_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGATCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MT291831_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_CHN_Beijing_IME_BJ01_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATATGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW493688_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_NMDOH_2021014099_2021_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGCGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGTAACCTTACAA + +>gb_MW559165_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2101316853_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTATCCAATTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW578122_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2101329819_2021_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTATCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTCTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW543034_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_AZ_CDC_IR9E_6611_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTATCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW053925_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_02760_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGCCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MT609578_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_VA_DCLS_0348_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTACAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW281864_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_West_Bank_Jericho_SARS_CoV_2_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAACGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW559163_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2101251032_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATAACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW067706_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_VA_DCLS_1288_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACACTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MT451174_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC278_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATCCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW589620_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_4464910_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTATCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW585995_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WV_CDC_STM_000003152_2021_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTATCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCTATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW577066_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_NMDOH_2021021590_2021_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTATTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW577930_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2101239410_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCCTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATTCTGGACAACAGGGCAACCTTACAA + +>gb_MW548941_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_S3648_2021_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAAATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MT380729_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_VI_CDC_1999_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGACACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW578256_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MO_CDC_2_3714171_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACCGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MT642069_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_S1116_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCCTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MT704128_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0028_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTGCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW228252_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_NMDOH_2020309735_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTGCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW517339_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_SC_COVID21_0044_2021_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCAGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW065141_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_IL_QDX_1100_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCCGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW064614_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MI_QDX_560_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTATTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW577730_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2101009422_2021_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGCTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MT969815_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC2996_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGGTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW571123_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_GHA_WACCBIP_nCoV_GS68_2021_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTCTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW586167_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_NC_CDC_STM_000005966_2021_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTGTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW467452_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_EGY_EGY_CCHE57357_A_44_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTGCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MT973439_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_TAS110_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATACAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW505146_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_QDX_3110_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAAGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW494399_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_BPHL_2779_2021_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGCGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW550186_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_QDX_4128_2021_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGCGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW518838_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MT_CDC_STM_227_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCCGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW577113_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_LACPHL_AF00314_2021_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTATAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW589574_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_4494168_2021_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTATAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACTTTACAA + +>gb_MT226610_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_CHN_KMS1_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTACACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW545441_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_LACPHL_AF00210_2021_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACACAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW562737_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2102453487_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAACTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW518128_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_AZ_CDC_STM_291_2021_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTGTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW586140_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_CDC_STM_000005978_2021_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTAAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW525001_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MI_CDC_STM_0000014_B04_2021_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAACGCTGGACAACAGGGCAACCTTACAA + +>gb_MW590718_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_IND_GBRC434_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGATGGACAACAGGGCAACCTTACAA + +>gb_MW467466_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_EGY_EGY_CCHE57357_A_58_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCCGGACAACAGGGCAACCTTACAA + +>gb_MW035538_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_UW_1372_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTAGACAACAGGGCAACCTTACAA + +>gb_MW474144_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_S2968_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTCGACAACAGGGCAACCTTACAA + +>gb_MW593460_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FHCRC_4649_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGAACAACAGGGCAACCTTACAA + +>gb_MW460617_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_QDX_2810_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGAGCAACCTTACAA + +>gb_MT470179_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_France_40002VJ_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGCGCAACCTTACAA + +>gb_MT856455_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_BCSIR_NILMRC_306_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCCTACAA + +>gb_MW067820_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_COVID20_1113_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAG + +>gb_MW483597_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_13466_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTGCAA + +>gb_MW156761_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC13590_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACTTTACAA + +>gb_MW276915_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC15878_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAATCTTACAA + +>gb_MT755838_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_BCSIR_NILMRC_245_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAGCCTTACAA + +>gb_MT446348_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_LA_BIE_080_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCGACCTTACAA + +>gb_MW550677_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_NJ_CDC_2_3768077_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCTACCTTACAA + +>gb_MW565664_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_13917_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGTAACCTTACAA + +>gb_MT460125_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_1105_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACGGGGCAACCTTACAA + +>gb_MW156759_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC13581_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAATAGGGCAACCTTACAA + +>gb_MW596107_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_000008078_2021_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAGCAGGGCAACCTTACAA + +>gb_MW564881_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_14887_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACGACAGGGCAACCTTACAA + +>gb_MW155687_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC13648_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGATAACAGGGCAACCTTACAA + +>gb_MW556183_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_IL_CDC_9MR4_8909_2021_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGGCAACAGGGCAACCTTACAA + +>gb_MT876607_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_BCSIR_NILMRC_291_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTTGACAACAGGGCAACCTTACAA + +>gb_MW521457_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_1516xF10_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGTTGGACAACAGGGCAACCTTACAA + +>gb_MT956712_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_BPHL_1102_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGTTGGATAACAGGGCAACCTTACAA + +>gb_MW521689_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_QDX_3455_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGACGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MT731735_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_BCSIR_NILMRC_137_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAGGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW593416_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FHCRC_880_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTTTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW599561_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_Broad_CRSP_00424_2021_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGTTTTGTGAAGAAATGCTGGATAACAGGGCAACCTTACAA + +>gb_MT451046_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC142_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAATCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW276413_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_10909_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAGGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MT810119_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_KOR_CNUHV03_CA22_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGCCATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW321295_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC17192_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTGGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW332236_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_RUS_2272_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGTGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW565288_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_14671_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCATGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW482871_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_GA_CDC_9H24_7433_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCATGGTGCTGTAGACATAAATAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW545201_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_QDX_3602_2021_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATTCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MT628119_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_1404_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCCTGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW127521_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_SRB_KS_0796_16_04_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCGTGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW495235_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_NH_QDX_3003_2021_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCTTGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW570895_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_LACPHL_AF00321_2021_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGTTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MT973055_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC6608_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTATTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW523832_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_AZ_CDC_STM_A100333_2021_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCATTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MT873107_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MGH_00733_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCGCTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW483436_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_12951_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTTACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW550562_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_DC_CDC_2_3773950_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATTGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW486275_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_UW_2499_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAGAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MT990449_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_EGY_CU001a_S1_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGGAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW539888_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_00651_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCTTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW565436_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_14349_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAGGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW586286_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_CDC_STM_000005415_2021_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTATTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW566520_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MO_QDX_4438_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTGCTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW596147_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_NC_CDC_STM_000008176_2021_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTGCTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAATCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW365025_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_CHL_Santiago_PUC_MVL_0397_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATATTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW566853_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_BPHL_2890_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATCCTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW596017_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_CDC_STM_000007226_2021_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAGAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW306408_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_12385_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGTTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW486330_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_UW_2532_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGTTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAATAGGGCAACCTTACAA + +>gb_MW583265_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_000001669_2021_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTTTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MT512423_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_VI_CDC_3688_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACGTTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW446829_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0493_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACGTTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAG + +>gb_MW030253_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_PER_covper022_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGATATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW276622_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_11799_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGATATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCTATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW539883_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_00646_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGATATTCTCTTAGCTAAAGATACTACTGAAGCTTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW341806_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_IL_UW_1937_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGATATTCTTTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MT451724_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC1057_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACATAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW517346_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_SC_COVID21_0036_2021_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACATAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGTTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW277478_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC16104_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCATTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MT612207_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC1606_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTTCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW527392_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_IRQ_NN_Erbil_2021_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTTCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGATATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW495176_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_QDX_2980_2021_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTTCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAGAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW406549_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_OK_CDC_2_3693789_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTTGCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAATCTTACAA + +>gb_MW483435_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_12950_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTTGCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGTTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAATCTTACAA + +>gb_MT499218_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_TUN_COV1663_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCACTGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW276537_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_11549_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCTATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW454734_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MGH_03468_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGTTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW420606_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2012663262_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATTTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAATAGGGCAACCTTACAA + +>gb_MW454728_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MGH_03452_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATTTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGTTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MT997720_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_1602_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCGTCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW181759_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_Homo_sapiens_HKG_Case4999_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATTATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW338802_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_VA_DCLS_2062_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATTATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACTTTACAA + +>gb_MW411628_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_VA_DCLS_2300_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATTATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAATCTTACAA + +>gb_MT786817_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_IN_QDX_182_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATTATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGTTGGACAACAGGGCAACCTTACAA + +>gb_MT966161_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_BPHL_0917_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATTATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAATAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MT981432_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_COVID20_0585_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATTATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGATATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MW067772_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_VA_DCLS_1293_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATTATCTAAATTGTGGGCTCAATGTGTCCAGTTACATAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MT992730_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_VA_DCLS_1113_2020_Segment_null_Host_Human +TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATTATCTAAATTGTGGGTTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA + +>gb_MT609579_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_VA_DCLS_0349_2020_Segment_null_Host_Human 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diversifying selection. \nAssuming there is evidence of positive selection (i.e. there is an omega > 1), BUSTED will also perform a quick evidence-ratio \nstyle analysis to explore which individual sites may have been subject to selection. v2.0 adds support for synonymous rate variation, \nand relaxes the test statistic to 0.5 (chi^2_0 + chi^2_2). Version 2.1 adds a grid search for the initial starting point.\nVersion 2.2 changes the grid search to LHC, and adds an initial search phase to use adaptive Nedler-Mead. Version 3.0 implements the option\nfor branch-site variation in synonymous substitution rates. 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112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197] + ], + "name":"busted.filter.default" + } + }, + "fits":{ + "Constrained model":{ + "AIC-c":2537.370055580011, + "Log Likelihood":-1205.042170647148, + "Rate Distributions":{ + "Background":{ + "0":{ + "omega":0.00623371489168318, + "proportion":0.02824597255703105 + }, + "1":{ + "omega":0.1719986773053319, + "proportion":0.8104926399157489 + }, + "2":{ + "omega":2.233103409549535, + "proportion":0.16126138752722 + } + }, + "Synonymous site-to-site rates":{ + "0":{ + "proportion":0, + "rate":0.9507923294014373 + }, + "1":{ + "proportion":1, + "rate":1 + }, + "2":{ 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order":0, + "estimated parameters":69 + }, + "Unconstrained model":{ + "AIC-c":2538.426858070025, + "Log Likelihood":-1204.550057961818, + "Rate Distributions":{ + "Background":{ + "0":{ + "omega":0, + "proportion":0.02741862862724963 + }, + "1":{ + "omega":0.1719979491289183, + "proportion":0.8111826871363725 + }, + "2":{ + "omega":2.232058479326601, + "proportion":0.1613986842363778 + } + }, + "Synonymous site-to-site rates":{ + "0":{ + "proportion":0, + "rate":0.9502886367487763 + }, + "1":{ + "proportion":1, + "rate":1 + }, + "2":{ + "proportion":0, + "rate":1.059678592887729 + } + }, + "Test":{ + "0":{ + "omega":0.9993684330797956, + "proportion":0 + }, + "1":{ + "omega":0.999368433118802, + "proportion":0 + }, + "2":{ + "omega":25.32658549655282, + "proportion":1 + } + } + }, + "display order":2, + "estimated parameters":64 + } + }, + "input":{ + "file name":"/home/aglucaci/SARS-CoV-2/clades/B-1-617/nsp8.combined.fas", + "number of sequences":32, + "number of sites":198, + "partition count":1, + "trees":{ + "0":"(REFERENCE,(gb_MT226610_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_CHN_KMS1_2020_Segment_null_Host_Human,epi_isl_1589870_hCoV_19_India_WB_1931501009078_2021)Node20,gb_MT326179_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_UW_1572_2020_Segment_null_Host_Human,epi_isl_1589885_hCoV_19_India_WB_1931300250528_2021,(epi_isl_1615709_hCoV_19_England_CAMC_14E792B_2021,gb_MW523870_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_LA_CDC_STM_A100279_2021_Segment_null_Host_Human)Node4,epi_isl_1592421_hCoV_19_USA_MA_CDC_STM_000044850_2021,gb_MW345265_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0448_2020_Segment_null_Host_Human,gb_MW525063_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MI_CDC_STM_0000013_D10_2021_Segment_null_Host_Human,epi_isl_1181694_hCoV_19_USA_DE_DHSS_B1064373_2021,gb_MW585851_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_GA_CDC_STM_000004152_2021_Segment_null_Host_Human,(gb_MW583322_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_AL_CDC_STM_000001665_2021_Segment_null_Host_Human,gb_MW562702_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2102128070_2020_Segment_null_Host_Human,epi_isl_1384851_hCoV_19_India_MH_NCCS_ND13683_2021)Node38,epi_isl_1357692_hCoV_19_India_WB_1931500870015_2021,gb_MW486334_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_UW_2535_2020_Segment_null_Host_Human,epi_isl_1533793_hCoV_19_India_MH_NCCS_CHN21027888_2021,gb_LR757997_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_UNKNOWN_LR757997_Segment_null_Host_Human,epi_isl_1415270_hCoV_19_India_MH_NCCS_BJ2_2021,epi_isl_1543980_hCoV_19_Singapore_490_2021,epi_isl_1632256_hCoV_19_England_RAND_14E1D70_2021,gb_MT745751_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_DNAS_isl_BRB_2020_Segment_null_Host_Human,epi_isl_1573247_hCoV_19_Germany_un_RKI_I_068985_2021,gb_MW585867_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_000003621_2021_Segment_null_Host_Human,gb_MW540189_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01215_2020_Segment_null_Host_Human,epi_isl_1652118_hCoV_19_Singapore_575_2021,epi_isl_1652105_hCoV_19_Singapore_561_2021,gb_MW593074_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2645_2021_Segment_null_Host_Human,gb_MW154124_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC7567_2020_Segment_null_Host_Human,epi_isl_1416968_hCoV_19_Guadeloupe_IPP06229_2021,epi_isl_1544068_hCoV_19_India_MH_NCCS_RT231527_2021)" + } + }, + "test results":{ + "LRT":0.9842253706597148, + "p-value":0.3056667368082906 + }, + "tested":{ + "0":{ + "Node20":"test", + "Node38":"background", + "Node4":"test", + "REFERENCE":"background", + "epi_isl_1181694_hCoV_19_USA_DE_DHSS_B1064373_2021":"background", + "epi_isl_1357692_hCoV_19_India_WB_1931500870015_2021":"background", + "epi_isl_1384851_hCoV_19_India_MH_NCCS_ND13683_2021":"background", + "epi_isl_1415270_hCoV_19_India_MH_NCCS_BJ2_2021":"background", + "epi_isl_1416968_hCoV_19_Guadeloupe_IPP06229_2021":"background", + "epi_isl_1533793_hCoV_19_India_MH_NCCS_CHN21027888_2021":"background", + "epi_isl_1543980_hCoV_19_Singapore_490_2021":"background", + "epi_isl_1544068_hCoV_19_India_MH_NCCS_RT231527_2021":"background", + "epi_isl_1573247_hCoV_19_Germany_un_RKI_I_068985_2021":"background", + "epi_isl_1589870_hCoV_19_India_WB_1931501009078_2021":"background", + "epi_isl_1589885_hCoV_19_India_WB_1931300250528_2021":"background", + "epi_isl_1592421_hCoV_19_USA_MA_CDC_STM_000044850_2021":"background", + "epi_isl_1615709_hCoV_19_England_CAMC_14E792B_2021":"background", + "epi_isl_1632256_hCoV_19_England_RAND_14E1D70_2021":"background", + "epi_isl_1652105_hCoV_19_Singapore_561_2021":"background", + "epi_isl_1652118_hCoV_19_Singapore_575_2021":"background", + "gb_LR757997_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_UNKNOWN_LR757997_Segment_null_Host_Human":"background", + "gb_MT226610_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_CHN_KMS1_2020_Segment_null_Host_Human":"background", + "gb_MT326179_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_UW_1572_2020_Segment_null_Host_Human":"background", + "gb_MT745751_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_DNAS_isl_BRB_2020_Segment_null_Host_Human":"background", + "gb_MW154124_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC7567_2020_Segment_null_Host_Human":"background", + "gb_MW345265_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0448_2020_Segment_null_Host_Human":"background", + "gb_MW486334_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_UW_2535_2020_Segment_null_Host_Human":"background", + "gb_MW523870_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_LA_CDC_STM_A100279_2021_Segment_null_Host_Human":"background", + "gb_MW525063_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MI_CDC_STM_0000013_D10_2021_Segment_null_Host_Human":"background", + "gb_MW540189_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01215_2020_Segment_null_Host_Human":"background", + "gb_MW562702_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2102128070_2020_Segment_null_Host_Human":"background", + "gb_MW583322_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_AL_CDC_STM_000001665_2021_Segment_null_Host_Human":"background", + "gb_MW585851_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_GA_CDC_STM_000004152_2021_Segment_null_Host_Human":"background", + "gb_MW585867_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_000003621_2021_Segment_null_Host_Human":"background", + "gb_MW593074_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2645_2021_Segment_null_Host_Human":"background" + } + }, + "timers":{ + "Constrained BUSTED model fitting":{ + "order":3, + "timer":3 + }, + "Overall":{ + "order":0, + "timer":76 + }, + "Preliminary model 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"Substitutions mapped to Reference branches"], + ["P-value (overall)", "P-value for the test that non-synonymous rates differ between any of the selected groups: B-1-617,Reference"], + ["Q-value (overall)", "Q-value for the test that non-synonymous rates differ between any of the selected groups: B-1-617,Reference"], + ["Permutation p-value", "Label permutation test for significant sites"], + ["Total branch length", "The total length of branches contributing to inference at this site, and used to scale beta-alpha"] + ] + }, + "analysis":{ + "authors":"Sergei L Kosakovsky Pond and Steven Weaver", + "citation":"TBD", + "contact":"spond@temple.edu", + "help":"http://www.hyphy.org/methods/other/contrast-fel/", + "info":"Contrast-FEL (Fixed Effects Likelihood) investigates whether or not selective pressures differ between two or more sets of\n branches at a site. Site-specific synonymous (alpha) and non-synonymous (beta, one per branch set) substitution rates are estimated\n and then beta rates are tested for equality at each site. LRT and permutation tests ar used to assess significance at each site, and FDR is applied alignment wide to call sites with different selective profiles", + "requirements":"in-frame codon alignment and a phylogenetic tree; only single partition data are supported", + "version":"0.5" + }, + "branch attributes":{ + "0":{ + "Node20":{ + "Global MG94xREV":0.001634892186392535, + "Nucleotide GTR":0.001684521619549293 + }, + "Node38":{ + "Global MG94xREV":0.001919664151147453, + "Nucleotide GTR":0.00168484920326581 + }, + "Node4":{ + "Global MG94xREV":0.001634608725470079, + "Nucleotide GTR":0.001683801387489096 + }, + "REFERENCE":{ + "Global MG94xREV":0, + "Nucleotide GTR":0, + "original name":"REFERENCE" + }, + "epi_isl_1181694_hCoV_19_USA_DE_DHSS_B1064373_2021":{ + "Global MG94xREV":0, + "Nucleotide GTR":0, + "original name":"epi_isl_1181694/hCoV-19/USA/DE-DHSS-B1064373/2021" + }, + "epi_isl_1357692_hCoV_19_India_WB_1931500870015_2021":{ + "Global MG94xREV":0.001728428286527107, + "Nucleotide GTR":0.001682745450340891, + "original name":"epi_isl_1357692/hCoV-19/India/WB-1931500870015/2021" + }, + "epi_isl_1384851_hCoV_19_India_MH_NCCS_ND13683_2021":{ + "Global MG94xREV":0, + "Nucleotide GTR":0, + "original name":"epi_isl_1384851/hCoV-19/India/MH-NCCS-ND13683/2021" + }, + "epi_isl_1415270_hCoV_19_India_MH_NCCS_BJ2_2021":{ + "Global MG94xREV":0.001727412680411063, + "Nucleotide GTR":0.00168274558227101, + "original name":"epi_isl_1415270/hCoV-19/India/MH-NCCS-BJ2/2021" + }, + "epi_isl_1416968_hCoV_19_Guadeloupe_IPP06229_2021":{ + "Global MG94xREV":0.001731169192232254, + "Nucleotide GTR":0.001684401404203384, + "original name":"epi_isl_1416968/hCoV-19/Guadeloupe/IPP06229/2021" + }, + "epi_isl_1533793_hCoV_19_India_MH_NCCS_CHN21027888_2021":{ + "Global MG94xREV":0.001728394297110263, + "Nucleotide GTR":0.00168406792173386, + "original name":"epi_isl_1533793/hCoV-19/India/MH-NCCS-CHN21027888/2021" + }, + "epi_isl_1543980_hCoV_19_Singapore_490_2021":{ + "Global 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"analysis":{ + "authors":"Sergei L Kosakovsky Pond and Simon DW Frost", + "citation":"Not So Different After All: A Comparison of Methods for Detecting Amino Acid Sites Under Selection (2005). _Mol Biol Evol_ 22 (5): 1208-1222", + "contact":"spond@temple.edu", + "info":"FEL (Fixed Effects Likelihood)\n estimates site-wise synonymous (α) and non-synonymous (β) rates, and\n uses a likelihood ratio test to determine if beta &neq; alpha at a site.\n The estimates aggregate information over all branches,\n so the signal is derived from\n pervasive diversification or conservation. A subset of branches can be selected\n for testing as well, in which case an additional (nuisance) parameter will be\n inferred -- the non-synonymous rate on branches NOT selected for testing.\n Multiple partitions within a NEXUS file are also supported\n for recombination - aware analysis.\n ", + "requirements":"in-frame codon alignment and a phylogenetic tree", + "version":"2.1" + }, + "branch attributes":{ + "0":{ + "Node20":{ + "Global MG94xREV":0.001634412620939209, + "Nucleotide GTR":0.001684521619549293 + }, + "Node38":{ + "Global MG94xREV":0.001735516186079463, + "Nucleotide GTR":0.00168484920326581 + }, + "Node4":{ + "Global MG94xREV":0.001634082124264937, + "Nucleotide GTR":0.001683801387489096 + }, + "REFERENCE":{ + "Global MG94xREV":0, + "Nucleotide GTR":0, + "original name":"REFERENCE" + }, + "epi_isl_1181694_hCoV_19_USA_DE_DHSS_B1064373_2021":{ + "Global MG94xREV":0, + "Nucleotide GTR":0, + "original name":"epi_isl_1181694/hCoV-19/USA/DE-DHSS-B1064373/2021" + }, + 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"gb_MW562702_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2102128070_2020_Segment_null_Host_Human":"background", + "gb_MW583322_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_AL_CDC_STM_000001665_2021_Segment_null_Host_Human":"background", + "gb_MW585851_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_GA_CDC_STM_000004152_2021_Segment_null_Host_Human":"background", + "gb_MW585867_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_000003621_2021_Segment_null_Host_Human":"background", + "gb_MW593074_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2645_2021_Segment_null_Host_Human":"background" + } + }, + "timers":{ + "FEL analysis":{ + "order":2, + "timer":4 + }, + "Model fitting":{ + "order":1, + "timer":6 + }, + "Total time":{ + "order":0, + "timer":10 + } + } +} \ No newline at end of file diff -r 5e8d0e777033 -r 60eec78ee26f test-data/summary/nsp8.MEME-full.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/nsp8.MEME-full.json Wed Jun 09 07:00:42 2021 +0000 @@ -0,0 +1,1796 @@ +{ + "MLE":{ + "content":{ + "0": [ +[0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0], + [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0], + [3.152554051843212, 0, 1, 4.728831077764818, 0, 0, 0.6666666666666666, 0, 0, -9.309130496877323, -9.309130496877323], + [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0], + [0, 0, 0.01, 11.93617095556557, 0.99, 1.181448599931173, 0.286224560648385, 1, 0, -8.156494645925976, -8.156780324191693], + [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0], + [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0], + [3.183060398629631, 0, 1, 4.774590597944442, 0, 0, 0.6666666666666666, 0, 0, -9.310784105780046, -9.310784105780046], + [0, 0, 0.001542572549341103, 9.536088848783528, 0.9984574274506589, 1.956236477088911, 0.1864481881457208, 1, 0, -9.131573461237856, -9.131799448740075], + [0, 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0.9729792144690599, 0.3226010900378987, 1, 0, -13.4656955178802, -13.46576611250398] + ] + }, + "headers": [ +["alpha;", "Synonymous substitution rate at a site"], + ["β-", "Non-synonymous substitution rate at a site for the negative/neutral evolution component"], + ["p-", "Mixture distribution weight allocated to β-; loosely -- the proportion of the tree evolving neutrally or under negative selection"], + ["β+", "Non-synonymous substitution rate at a site for the positive/neutral evolution component"], + ["p+", "Mixture distribution weight allocated to β+; loosely -- the proportion of the tree evolving neutrally or under positive selection"], + ["LRT", "Likelihood ratio test statistic for episodic diversification, i.e., p+ > 0 and β+ > α"], + ["p-value", "Asymptotic p-value for episodic diversification, i.e., p+ > 0 and β+ > α"], + ["# branches under selection", "The (very approximate and rough) estimate of how many branches may have been under selection at this site, i.e., had an empirical Bayes factor of 100 or more for the β+ rate"], + ["Total branch length", "The total length of branches contributing to inference at this site, and used to scale dN-dS"], + ["MEME LogL", "Site Log-likelihood under the MEME model"], + ["FEL LogL", "Site Log-likelihood under the FEL model"] + ] + }, + "analysis":{ + "authors":"Sergei L. Kosakovsky Pond, Steven Weaver", + "citation":"Detecting Individual Sites Subject to Episodic Diversifying Selection. _PLoS Genet_ 8(7): e1002764.", + "contact":"spond@temple.edu", + "info":"MEME (Mixed Effects Model of Evolution)\n estimates a site-wise synonymous (α) and a two-category mixture of non-synonymous\n (β-, with proportion p-, and β+ with proportion [1-p-]) rates, and\n uses a likelihood ratio test to determine if β+ > α at a site.\n The estimates aggregate information over a proportion of branches at a site,\n so the signal is derived from\n episodic diversification, which is a combination of strength of selection [effect size] and\n the proportion of the tree affected. A subset of branches can be selected\n for testing as well, in which case an additional (nuisance) parameter will be\n inferred -- the non-synonymous rate on branches NOT selected for testing. Multiple partitions within a NEXUS file are also supported\n for recombination - aware analysis.\n ", + "requirements":"in-frame codon alignment and a phylogenetic tree", + "version":"2.1.2" + }, + "branch attributes":{ + "0":{ + "Node20":{ + "EBF site 101 (partition 1)":1, + "EBF site 103 (partition 1)":1, + "EBF site 116 (partition 1)":1, + "EBF site 123 (partition 1)":0.9318057941714948, + "EBF site 125 (partition 1)":1, + "EBF site 126 (partition 1)":1, + "EBF site 128 (partition 1)":1, + "EBF site 133 (partition 1)":0.9302605239852906, + "EBF site 134 (partition 1)":1, + "EBF site 14 (partition 1)":1, + "EBF site 140 (partition 1)":1, + "EBF site 141 (partition 1)":1, + "EBF site 145 (partition 1)":1, + "EBF site 146 (partition 1)":0.9318057941715044, + "EBF site 148 (partition 1)":1, + "EBF site 15 (partition 1)":1, + "EBF site 156 (partition 1)":1, + "EBF site 16 (partition 1)":1, + "EBF site 160 (partition 1)":1, + "EBF site 161 (partition 1)":1, + "EBF site 163 (partition 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> α"], + ["p-value", "Asymptotic p-value for episodic diversification, i.e., p+ > 0 and β+ > α"], + ["# branches under selection", "The (very approximate and rough) estimate of how many branches may have been under selection at this site, i.e., had an empirical Bayes factor of 100 or more for the β+ rate"], + ["Total branch length", "The total length of branches contributing to inference at this site, and used to scale dN-dS"], + ["MEME LogL", "Site Log-likelihood under the MEME model"], + ["FEL LogL", "Site Log-likelihood under the FEL model"] + ] + }, + "analysis":{ + "authors":"Sergei L. Kosakovsky Pond, Steven Weaver", + "citation":"Detecting Individual Sites Subject to Episodic Diversifying Selection. _PLoS Genet_ 8(7): e1002764.", + "contact":"spond@temple.edu", + "info":"MEME (Mixed Effects Model of Evolution)\n estimates a site-wise synonymous (α) and a two-category mixture of non-synonymous\n (β-, with proportion p-, and β+ with proportion [1-p-]) rates, and\n uses a likelihood ratio test to determine if β+ > α at a site.\n The estimates aggregate information over a proportion of branches at a site,\n so the signal is derived from\n episodic diversification, which is a combination of strength of selection [effect size] and\n the proportion of the tree affected. A subset of branches can be selected\n for testing as well, in which case an additional (nuisance) parameter will be\n inferred -- the non-synonymous rate on branches NOT selected for testing. Multiple partitions within a NEXUS file are also supported\n for recombination - aware analysis.\n ", + "requirements":"in-frame codon alignment and a phylogenetic tree", + "version":"2.1.2" + }, + "branch attributes":{ + "0":{ + "Node20":{ + "EBF site 101 (partition 1)":1, + "EBF site 103 (partition 1)":1, + "EBF site 116 (partition 1)":1, + "EBF site 123 (partition 1)":1, + "EBF site 125 (partition 1)":0.9999823899944797, + "EBF site 126 (partition 1)":1, + "EBF site 128 (partition 1)":1, + "EBF site 133 (partition 1)":0.5654898147900533, + "EBF site 134 (partition 1)":1, + "EBF site 14 (partition 1)":1, + "EBF site 140 (partition 1)":1, + "EBF site 141 (partition 1)":1, + "EBF site 145 (partition 1)":1, + "EBF site 146 (partition 1)":1, + "EBF site 148 (partition 1)":1, + "EBF site 15 (partition 1)":1, + "EBF site 156 (partition 1)":1, + "EBF site 16 (partition 1)":1, + "EBF site 160 (partition 1)":1, + "EBF site 161 (partition 1)":1, + "EBF site 163 (partition 1)":1, + "EBF site 164 (partition 1)":1, + "EBF site 170 (partition 1)":1, + "EBF site 176 (partition 1)":1, + "EBF site 179 (partition 1)":1, + "EBF site 18 (partition 1)":1, + "EBF site 187 (partition 1)":1, + "EBF site 190 (partition 1)":1, + "EBF site 198 (partition 1)":1, + "EBF site 21 (partition 1)":1, + "EBF site 23 (partition 1)":1, + "EBF site 25 (partition 1)":1, + "EBF site 27 (partition 1)":1, + "EBF site 3 (partition 1)":1, + "EBF site 30 (partition 1)":1, + "EBF site 37 (partition 1)":1616.162948531769, + "EBF site 39 (partition 1)":1, + "EBF site 40 (partition 1)":1, + "EBF site 5 (partition 1)":1, + "EBF site 51 (partition 1)":0.9995339403671608, + "EBF site 63 (partition 1)":1, + "EBF site 67 (partition 1)":1, + "EBF site 70 (partition 1)":1, + "EBF site 73 (partition 1)":1, + "EBF site 74 (partition 1)":1, + "EBF site 76 (partition 1)":1, + "EBF site 8 (partition 1)":1, + "EBF site 81 (partition 1)":1, + "EBF site 83 (partition 1)":1, + "EBF site 85 (partition 1)":0.9998333727208876, + 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1)":1, + "EBF site 160 (partition 1)":1, + "EBF site 161 (partition 1)":1, + "EBF site 163 (partition 1)":1, + "EBF site 164 (partition 1)":1, + "EBF site 170 (partition 1)":1, + "EBF site 176 (partition 1)":1, + "EBF site 179 (partition 1)":1, + "EBF site 18 (partition 1)":1, + "EBF site 187 (partition 1)":1, + "EBF site 190 (partition 1)":1, + "EBF site 198 (partition 1)":1, + "EBF site 21 (partition 1)":1, + "EBF site 23 (partition 1)":1, + "EBF site 25 (partition 1)":1, + "EBF site 27 (partition 1)":1, + "EBF site 3 (partition 1)":1, + "EBF site 30 (partition 1)":1, + "EBF site 37 (partition 1)":0.5725438663972433, + "EBF site 39 (partition 1)":1, + "EBF site 40 (partition 1)":1, + "EBF site 5 (partition 1)":1, + "EBF site 51 (partition 1)":0.9995340347254161, + "EBF site 63 (partition 1)":1, + "EBF site 67 (partition 1)":1, + "EBF site 70 (partition 1)":1, + "EBF site 73 (partition 1)":1, + "EBF site 74 (partition 1)":1, + "EBF site 76 (partition 1)":1, + "EBF site 8 (partition 1)":1, + "EBF site 81 (partition 1)":1, + "EBF site 83 (partition 1)":1, + "EBF site 85 (partition 1)":0.9998334064611279, + "EBF site 88 (partition 1)":1, + "EBF site 89 (partition 1)":1, + "EBF site 9 (partition 1)":1, + "EBF site 96 (partition 1)":0.9999780801079843, + "EBF site 99 (partition 1)":1, + "Global MG94xREV":0.001634082124753167, + "Nucleotide GTR":0.001683801387489096 + }, + "REFERENCE":{ + "Global MG94xREV":0, + "Nucleotide GTR":0, + "original name":"REFERENCE" + }, + "epi_isl_1181694_hCoV_19_USA_DE_DHSS_B1064373_2021":{ + "Global MG94xREV":0, + "Nucleotide GTR":0, + "original name":"epi_isl_1181694/hCoV-19/USA/DE-DHSS-B1064373/2021" + }, + "epi_isl_1357692_hCoV_19_India_WB_1931500870015_2021":{ + "Global MG94xREV":0.001732287228161539, + "Nucleotide GTR":0.001682745450340891, + "original name":"epi_isl_1357692/hCoV-19/India/WB-1931500870015/2021" + }, + "epi_isl_1384851_hCoV_19_India_MH_NCCS_ND13683_2021":{ + "Global MG94xREV":0, + "Nucleotide GTR":0, + "original name":"epi_isl_1384851/hCoV-19/India/MH-NCCS-ND13683/2021" + }, + "epi_isl_1415270_hCoV_19_India_MH_NCCS_BJ2_2021":{ + "Global MG94xREV":0.001731614560044905, + "Nucleotide GTR":0.00168274558227101, + "original name":"epi_isl_1415270/hCoV-19/India/MH-NCCS-BJ2/2021" + }, + "epi_isl_1416968_hCoV_19_Guadeloupe_IPP06229_2021":{ + "Global MG94xREV":0.001735723691511758, + "Nucleotide GTR":0.001684401404203384, + "original name":"epi_isl_1416968/hCoV-19/Guadeloupe/IPP06229/2021" + }, + "epi_isl_1533793_hCoV_19_India_MH_NCCS_CHN21027888_2021":{ + "Global MG94xREV":0.001732400226671219, + "Nucleotide GTR":0.00168406792173386, + "original name":"epi_isl_1533793/hCoV-19/India/MH-NCCS-CHN21027888/2021" + }, + "epi_isl_1543980_hCoV_19_Singapore_490_2021":{ + "Global MG94xREV":0.001734572373969102, + "Nucleotide GTR":0.001684975469042935, + "original name":"epi_isl_1543980/hCoV-19/Singapore/490/2021" + }, + "epi_isl_1544068_hCoV_19_India_MH_NCCS_RT231527_2021":{ + "Global MG94xREV":0.001735567214549057, + "Nucleotide GTR":0.001684401583391051, + "original name":"epi_isl_1544068/hCoV-19/India/MH-NCCS-RT231527/2021" + }, + "epi_isl_1573247_hCoV_19_Germany_un_RKI_I_068985_2021":{ + "Global MG94xREV":0.001732287292348436, + "Nucleotide GTR":0.001682745512695379, + "original name":"epi_isl_1573247/hCoV-19/Germany/un-RKI-I-068985/2021" + }, + "epi_isl_1589870_hCoV_19_India_WB_1931501009078_2021":{ + "Global MG94xREV":0, + "Nucleotide GTR":0, + "original name":"epi_isl_1589870/hCoV-19/India/WB-1931501009078/2021" + }, + "epi_isl_1589885_hCoV_19_India_WB_1931300250528_2021":{ + "Global MG94xREV":0.001733756931612698, + "Nucleotide GTR":0.001684431017860219, + "original name":"epi_isl_1589885/hCoV-19/India/WB-1931300250528/2021" + }, + "epi_isl_1592421_hCoV_19_USA_MA_CDC_STM_000044850_2021":{ + "Global MG94xREV":0.001733765374593157, + "Nucleotide GTR":0.001684439221071522, + "original name":"epi_isl_1592421/hCoV-19/USA/MA-CDC-STM-000044850/2021" + }, + 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-13.77239892102621, 1, 0.03644798756061563, 1, -13.77190817477141, -0.3104805457700024, 1, -13.77191376864584, 0.2357212180710769, 1, -13.77190817477141, -0.03138277695602196, 1, -13.77191376864584, -0.005528760550374304, 1, -13.7719081747714] + ] + }, + "headers": [ +["alpha;", "Synonymous substitution rate at a site"], + ["β", "Log of property independent non-synonymous rate a site"], + ["Total branch length", "The total length of branches contributing to inference at this site, and used to scale dN-dS"], + ["PRIME LogL", "Site Log-likelihood under the PRIME model"], + ["FEL LogL", "Site Log-likelihood under the FEL model"], + ["p-value", "Omnibus p-value (any property is important)"], + ["λ1", "Importance for Factor I bipolar"], + ["p1", "p-value for non-zero effect of Factor I bipolar"], + ["LogL1", "Log likelihood when there is no effect of Factor I bipolar"], + ["λ2", "Importance for Factor II secondary structure"], + ["p2", "p-value for non-zero effect of Factor II secondary structure"], + ["LogL2", "Log likelihood when there is no effect of Factor II secondary structure"], + ["λ3", "Importance for Factor III volume"], + ["p3", "p-value for non-zero effect of Factor III volume"], + ["LogL3", "Log likelihood when there is no effect of Factor III volume"], + ["λ4", "Importance for Factor IV composition"], + ["p4", "p-value for non-zero effect of Factor IV composition"], + ["LogL4", "Log likelihood when there is no effect of Factor IV composition"], + ["λ5", "Importance for Factor V charge"], + ["p5", "p-value for non-zero effect of Factor V charge"], + ["LogL5", "Log likelihood when there is no effect of Factor V charge"] + ] + }, + "analysis":{ + "authors":"Sergei L. Kosakovsky Pond", + "citation":"TBD", + "contact":"spond@temple.edu", + "info":"PRIME (PRoperty Informed Model of Evolution). Given a set of N amino-acid properties,\n fit a site-level model where non-synonymous rates depend on how much a non-synonymous substitution changes the \n properties of the residue, beta (X,Y) = Exp (log_omega - lambda_1 * diff_1 (X,Y )- lambda_2 * diff_2 (X,Y) -...).\n When lambda_k > 0, changes in property k are disfavored and when lambda_k < 0 -- they are promoted.\n At each site, N tests are performed\n A subset of branches can be selected\n for testing as well, in which case an additional (nuisance) parameter will be\n inferred -- the non-synonymous rate on branches NOT selected for testing. Multiple partitions within a NEXUS file are also supported\n for recombination - aware analysis.\n ", + "requirements":"in-frame codon alignment and a phylogenetic tree", + "version":"0.0.1" + }, + "branch attributes":{ + "0":{ + "Node20":{ + "Global MG94xREV":0.001634412628363601, + "Nucleotide GTR":0.001684521619549293 + }, + "Node38":{ + "Global MG94xREV":0.001735516181127408, + "Nucleotide GTR":0.00168484920326581 + }, + "Node4":{ + "Global MG94xREV":0.001634082125054255, + "Nucleotide GTR":0.001683801387489096 + }, + "REFERENCE":{ + "Global MG94xREV":0, + "Nucleotide GTR":0, + "original name":"REFERENCE" + }, + "epi_isl_1181694_hCoV_19_USA_DE_DHSS_B1064373_2021":{ + "Global MG94xREV":0, + "Nucleotide GTR":0, + "original name":"epi_isl_1181694/hCoV-19/USA/DE-DHSS-B1064373/2021" + }, + "epi_isl_1357692_hCoV_19_India_WB_1931500870015_2021":{ + "Global MG94xREV":0.001732287226413535, + "Nucleotide GTR":0.001682745450340891, + "original name":"epi_isl_1357692/hCoV-19/India/WB-1931500870015/2021" + }, + "epi_isl_1384851_hCoV_19_India_MH_NCCS_ND13683_2021":{ + "Global MG94xREV":0, + "Nucleotide GTR":0, + "original name":"epi_isl_1384851/hCoV-19/India/MH-NCCS-ND13683/2021" + }, + "epi_isl_1415270_hCoV_19_India_MH_NCCS_BJ2_2021":{ + "Global MG94xREV":0.001731614558297581, + "Nucleotide GTR":0.00168274558227101, + "original name":"epi_isl_1415270/hCoV-19/India/MH-NCCS-BJ2/2021" + }, + "epi_isl_1416968_hCoV_19_Guadeloupe_IPP06229_2021":{ + "Global MG94xREV":0.001735723689760284, + "Nucleotide GTR":0.001684401404203384, + "original name":"epi_isl_1416968/hCoV-19/Guadeloupe/IPP06229/2021" + }, + "epi_isl_1533793_hCoV_19_India_MH_NCCS_CHN21027888_2021":{ + "Global MG94xREV":0.001732400224923104, + "Nucleotide GTR":0.00168406792173386, + "original name":"epi_isl_1533793/hCoV-19/India/MH-NCCS-CHN21027888/2021" + }, + "epi_isl_1543980_hCoV_19_Singapore_490_2021":{ + "Global MG94xREV":0.001734572372218793, + "Nucleotide GTR":0.001684975469042935, + "original name":"epi_isl_1543980/hCoV-19/Singapore/490/2021" + }, + "epi_isl_1544068_hCoV_19_India_MH_NCCS_RT231527_2021":{ + "Global MG94xREV":0.001735567212797747, + "Nucleotide GTR":0.001684401583391051, + "original name":"epi_isl_1544068/hCoV-19/India/MH-NCCS-RT231527/2021" + }, + "epi_isl_1573247_hCoV_19_Germany_un_RKI_I_068985_2021":{ + "Global MG94xREV":0.001732287290600434, + "Nucleotide GTR":0.001682745512695379, + "original name":"epi_isl_1573247/hCoV-19/Germany/un-RKI-I-068985/2021" + }, + "epi_isl_1589870_hCoV_19_India_WB_1931501009078_2021":{ + "Global MG94xREV":0, + "Nucleotide GTR":0, + "original name":"epi_isl_1589870/hCoV-19/India/WB-1931501009078/2021" + }, + "epi_isl_1589885_hCoV_19_India_WB_1931300250528_2021":{ + "Global MG94xREV":0.001733756929863212, + "Nucleotide GTR":0.001684431017860219, + "original name":"epi_isl_1589885/hCoV-19/India/WB-1931300250528/2021" + }, + "epi_isl_1592421_hCoV_19_USA_MA_CDC_STM_000044850_2021":{ + "Global MG94xREV":0.001733765372843661, + "Nucleotide GTR":0.001684439221071522, + "original name":"epi_isl_1592421/hCoV-19/USA/MA-CDC-STM-000044850/2021" + }, + "epi_isl_1615709_hCoV_19_England_CAMC_14E792B_2021":{ + "Global MG94xREV":0, + "Nucleotide GTR":0, + "original name":"epi_isl_1615709/hCoV-19/England/CAMC-14E792B/2021" + }, + "epi_isl_1632256_hCoV_19_England_RAND_14E1D70_2021":{ + "Global MG94xREV":0.001736016199323374, + "Nucleotide GTR":0.00168443927661716, + "original name":"epi_isl_1632256/hCoV-19/England/RAND-14E1D70/2021" + }, + "epi_isl_1652105_hCoV_19_Singapore_561_2021":{ + "Global MG94xREV":0.001733699172098583, + "Nucleotide GTR":0.001685171120971631, + "original name":"epi_isl_1652105/hCoV-19/Singapore/561/2021" + }, + "epi_isl_1652118_hCoV_19_Singapore_575_2021":{ + "Global MG94xREV":0.001733317353440973, + "Nucleotide GTR":0.001684401899924961, + "original name":"epi_isl_1652118/hCoV-19/Singapore/575/2021" + }, + 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"Nucleotide GTR":0.003373764235314068, + "original name":"gb_MW523870_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_LA_CDC_STM_A100279_2021_Segment_null_Host_Human" + }, + "gb_MW525063_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MI_CDC_STM_0000013_D10_2021_Segment_null_Host_Human":{ + "Global MG94xREV":0.005236219925335357, + "Nucleotide GTR":0.005068409188375663, + "original name":"gb_MW525063_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MI_CDC_STM_0000013_D10_2021_Segment_null_Host_Human" + }, + "gb_MW540189_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01215_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0.003464842721718857, + "Nucleotide GTR":0.003372774424770855, + "original 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+ } + }, + "tested":{ + "0":{ + "Node20":"test", + "Node38":"background", + "Node4":"test", + "REFERENCE":"background", + "epi_isl_1181694_hCoV_19_USA_DE_DHSS_B1064373_2021":"background", + "epi_isl_1357692_hCoV_19_India_WB_1931500870015_2021":"background", + "epi_isl_1384851_hCoV_19_India_MH_NCCS_ND13683_2021":"background", + "epi_isl_1415270_hCoV_19_India_MH_NCCS_BJ2_2021":"background", + "epi_isl_1416968_hCoV_19_Guadeloupe_IPP06229_2021":"background", + "epi_isl_1533793_hCoV_19_India_MH_NCCS_CHN21027888_2021":"background", + "epi_isl_1543980_hCoV_19_Singapore_490_2021":"background", + "epi_isl_1544068_hCoV_19_India_MH_NCCS_RT231527_2021":"background", + "epi_isl_1573247_hCoV_19_Germany_un_RKI_I_068985_2021":"background", + "epi_isl_1589870_hCoV_19_India_WB_1931501009078_2021":"background", + "epi_isl_1589885_hCoV_19_India_WB_1931300250528_2021":"background", + "epi_isl_1592421_hCoV_19_USA_MA_CDC_STM_000044850_2021":"background", + "epi_isl_1615709_hCoV_19_England_CAMC_14E792B_2021":"background", + "epi_isl_1632256_hCoV_19_England_RAND_14E1D70_2021":"background", + "epi_isl_1652105_hCoV_19_Singapore_561_2021":"background", + "epi_isl_1652118_hCoV_19_Singapore_575_2021":"background", + "gb_LR757997_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_UNKNOWN_LR757997_Segment_null_Host_Human":"background", + "gb_MT226610_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_CHN_KMS1_2020_Segment_null_Host_Human":"background", + "gb_MT326179_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_UW_1572_2020_Segment_null_Host_Human":"background", + "gb_MT745751_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_DNAS_isl_BRB_2020_Segment_null_Host_Human":"background", + 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branch sets":{ + "AIC-c":2512.992528250552, + "Equilibrium frequencies": [ +[0.03825952761243274], + [0.01370948533169502], + [0.0238326285579188], + [0.05169206288834598], + [0.02910782227384961], + [0.01043016700423795], + [0.01813184740308045], + [0.03932728586627101], + [0.01035067712195123], + [0.003708944282165923], + [0.006447644771501305], + [0.01398469573761802], + [0.0283653688047424], + [0.01016412464618009], + [0.01766935821790241], + [0.03832416445281453], + [0.01521889661505549], + [0.005453366858635389], + [0.009480156518454269], + [0.02056209812326697], + [0.01157852606970437], + [0.004148917752546374], + [0.007212496554133422], + [0.01564363009947405], + [0.00411729822204095], + [0.001475345962268018], + [0.002564747797779777], + [0.005562840210150803], + [0.01128319250724396], + [0.004043091272315801], + [0.007028527343480687], + [0.01524460789411934], + [0.03592403244011121], + [0.01287261047188149], + [0.02237780168434643], + [0.04853659885475865], + 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+ }, + "Nucleotide GTR":{ + "AIC-c":2633.0046471406, + "Equilibrium frequencies": [ +[0.3251262626262627], + [0.1799242424242424], + [0.2026515151515151], + [0.2922979797979798] + ], + "Log Likelihood":-1247.247280799152, + "Rate Distributions":{ + "Substitution rate from nucleotide A to nucleotide C":0, + "Substitution rate from nucleotide A to nucleotide G":1, + "Substitution rate from nucleotide A to nucleotide T":0.3101631549852981, + "Substitution rate from nucleotide C to nucleotide G":1.129990583516242, + "Substitution rate from nucleotide C to nucleotide T":2.723444388603395, + "Substitution rate from nucleotide G to nucleotide T":1.720896006888861 + }, + "display order":0, + "estimated parameters":69 + }, + "RELAX alternative":{ + "AIC-c":2539.023758734034, + "Log Likelihood":-1203.827668840701, + "Rate Distributions":{ + "Reference":{ + "0":{ + "omega":0, + "proportion":0.3229316344832856 + }, + "1":{ + "omega":0, + "proportion":0.6561871399951409 + }, + "2":{ + "omega":2.618905128891877, + "proportion":0.02088122552157349 + } + }, + "Synonymous site-to-site rates":{ + "0":{ + "proportion":0, + "rate":0.8672539109745554 + }, + "1":{ + "proportion":1, + "rate":1 + }, + "2":{ + "proportion":0, + "rate":1.04385559910209 + } + }, + "Test":{ + "0":{ + "omega":0, + "proportion":0.3229316344832856 + }, + "1":{ + "omega":0, + "proportion":0.6561871399951409 + }, + "2":{ + "omega":887.8019782663979, + "proportion":0.02088122552157349 + } + } + }, + "display order":2, + "estimated parameters":65 + }, + "RELAX null":{ + "AIC-c":2540.205243445127, + "Log Likelihood":-1205.43925064937, + "Rate Distributions":{ + "Reference":{ + "0":{ + "omega":0.01761845549263694, + "proportion":0.1028887690453239 + }, + "1":{ + "omega":0.1789488803563501, + "proportion":0.8141260406522884 + }, + "2":{ + "omega":5.480099329809248, + "proportion":0.08298519030238755 + } + }, + "Synonymous site-to-site rates":{ + "0":{ + "proportion":0, + "rate":0.8690455710978635 + }, + "1":{ + "proportion":1, + "rate":1 + }, + "2":{ + "proportion":0, + "rate":1.043145103957073 + } + }, + "Test":{ + "0":{ + "omega":0.01761845549263694, + "proportion":0.1028887690453239 + }, + "1":{ + "omega":0.1789488803563501, + "proportion":0.8141260406522884 + }, + "2":{ + "omega":5.480099329809248, + "proportion":0.08298519030238755 + } + } + }, + "display order":3, + "estimated parameters":64 + } + }, + "input":{ + "file name":"/home/aglucaci/SARS-CoV-2/clades/B-1-617/nsp8.combined.fas", + "number of sequences":32, + "number of sites":198, + "partition count":1, + "trees":{ + "0":"(REFERENCE,(gb_MT226610_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_CHN_KMS1_2020_Segment_null_Host_Human,epi_isl_1589870_hCoV_19_India_WB_1931501009078_2021)Node20,gb_MT326179_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_UW_1572_2020_Segment_null_Host_Human,epi_isl_1589885_hCoV_19_India_WB_1931300250528_2021,(epi_isl_1615709_hCoV_19_England_CAMC_14E792B_2021,gb_MW523870_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_LA_CDC_STM_A100279_2021_Segment_null_Host_Human)Node4,epi_isl_1592421_hCoV_19_USA_MA_CDC_STM_000044850_2021,gb_MW345265_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0448_2020_Segment_null_Host_Human,gb_MW525063_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MI_CDC_STM_0000013_D10_2021_Segment_null_Host_Human,epi_isl_1181694_hCoV_19_USA_DE_DHSS_B1064373_2021,gb_MW585851_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_GA_CDC_STM_000004152_2021_Segment_null_Host_Human,(gb_MW583322_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_AL_CDC_STM_000001665_2021_Segment_null_Host_Human,gb_MW562702_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2102128070_2020_Segment_null_Host_Human,epi_isl_1384851_hCoV_19_India_MH_NCCS_ND13683_2021)Node38,epi_isl_1357692_hCoV_19_India_WB_1931500870015_2021,gb_MW486334_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_UW_2535_2020_Segment_null_Host_Human,epi_isl_1533793_hCoV_19_India_MH_NCCS_CHN21027888_2021,gb_LR757997_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_UNKNOWN_LR757997_Segment_null_Host_Human,epi_isl_1415270_hCoV_19_India_MH_NCCS_BJ2_2021,epi_isl_1543980_hCoV_19_Singapore_490_2021,epi_isl_1632256_hCoV_19_England_RAND_14E1D70_2021,gb_MT745751_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_DNAS_isl_BRB_2020_Segment_null_Host_Human,epi_isl_1573247_hCoV_19_Germany_un_RKI_I_068985_2021,gb_MW585867_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_000003621_2021_Segment_null_Host_Human,gb_MW540189_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01215_2020_Segment_null_Host_Human,epi_isl_1652118_hCoV_19_Singapore_575_2021,epi_isl_1652105_hCoV_19_Singapore_561_2021,gb_MW593074_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2645_2021_Segment_null_Host_Human,gb_MW154124_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC7567_2020_Segment_null_Host_Human,epi_isl_1416968_hCoV_19_Guadeloupe_IPP06229_2021,epi_isl_1544068_hCoV_19_India_MH_NCCS_RT231527_2021)" + } + }, + "test results":{ + "LRT":3.223163617336922, + "p-value":0.07260318641568564, + "relaxation or intensification parameter":7.051367447513434 + }, + "tested":{ + "0":{ + "Node20":"Test", + "Node38":"Reference", + "Node4":"Test", + "REFERENCE":"Unclassified", + "epi_isl_1181694_hCoV_19_USA_DE_DHSS_B1064373_2021":"Unclassified", + "epi_isl_1357692_hCoV_19_India_WB_1931500870015_2021":"Unclassified", + "epi_isl_1384851_hCoV_19_India_MH_NCCS_ND13683_2021":"Unclassified", + "epi_isl_1415270_hCoV_19_India_MH_NCCS_BJ2_2021":"Unclassified", + "epi_isl_1416968_hCoV_19_Guadeloupe_IPP06229_2021":"Unclassified", + "epi_isl_1533793_hCoV_19_India_MH_NCCS_CHN21027888_2021":"Unclassified", + "epi_isl_1543980_hCoV_19_Singapore_490_2021":"Unclassified", + "epi_isl_1544068_hCoV_19_India_MH_NCCS_RT231527_2021":"Unclassified", + "epi_isl_1573247_hCoV_19_Germany_un_RKI_I_068985_2021":"Unclassified", + "epi_isl_1589870_hCoV_19_India_WB_1931501009078_2021":"Unclassified", + "epi_isl_1589885_hCoV_19_India_WB_1931300250528_2021":"Unclassified", + "epi_isl_1592421_hCoV_19_USA_MA_CDC_STM_000044850_2021":"Unclassified", + "epi_isl_1615709_hCoV_19_England_CAMC_14E792B_2021":"Unclassified", + "epi_isl_1632256_hCoV_19_England_RAND_14E1D70_2021":"Unclassified", + "epi_isl_1652105_hCoV_19_Singapore_561_2021":"Unclassified", + "epi_isl_1652118_hCoV_19_Singapore_575_2021":"Unclassified", + "gb_LR757997_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_UNKNOWN_LR757997_Segment_null_Host_Human":"Unclassified", + "gb_MT226610_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_CHN_KMS1_2020_Segment_null_Host_Human":"Unclassified", + "gb_MT326179_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_UW_1572_2020_Segment_null_Host_Human":"Unclassified", + "gb_MT745751_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_DNAS_isl_BRB_2020_Segment_null_Host_Human":"Unclassified", + "gb_MW154124_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC7567_2020_Segment_null_Host_Human":"Unclassified", + "gb_MW345265_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0448_2020_Segment_null_Host_Human":"Unclassified", + "gb_MW486334_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_UW_2535_2020_Segment_null_Host_Human":"Unclassified", + "gb_MW523870_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_LA_CDC_STM_A100279_2021_Segment_null_Host_Human":"Unclassified", + "gb_MW525063_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MI_CDC_STM_0000013_D10_2021_Segment_null_Host_Human":"Unclassified", + "gb_MW540189_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01215_2020_Segment_null_Host_Human":"Unclassified", + "gb_MW562702_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2102128070_2020_Segment_null_Host_Human":"Unclassified", + "gb_MW583322_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_AL_CDC_STM_000001665_2021_Segment_null_Host_Human":"Unclassified", + "gb_MW585851_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_GA_CDC_STM_000004152_2021_Segment_null_Host_Human":"Unclassified", + "gb_MW585867_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_000003621_2021_Segment_null_Host_Human":"Unclassified", + "gb_MW593074_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2645_2021_Segment_null_Host_Human":"Unclassified" + } + }, + "timers":{ + "Overall":{ + "order":0, + "timer":67 + }, + "Preliminary model fitting":{ + "order":1, + "timer":5 + }, + "RELAX alternative model fitting":{ + "order":3, + "timer":50 + }, + "RELAX null model fitting":{ + "order":4, + "timer":12 + } + } +} \ No newline at end of file diff -r 5e8d0e777033 -r 60eec78ee26f test-data/summary/nsp8.SLAC.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/nsp8.SLAC.json Wed Jun 09 07:00:42 2021 +0000 @@ -0,0 +1,1350 @@ +{ + "MLE":{ + "content":{ + "0":{ + "by-branch":{ + "AVERAGED": [ +[0, 0, 0, 0, null, null, null, null, 1, 1, 0], + [147.0112938906491, 421.9561434851458, 2, 13, 0.2583826142471318, 0.01360439696209771, 0.03080888902961936, 0.1540517400002438, 0.2141909453461294, 0.9297070045663574, 0.02664074934348415], + [0, 0, 0, 0, null, null, null, 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substitutions"], + ["P[S]", "Expected proportion of synonymous sites"], + ["dS", "Inferred synonymous susbsitution rate"], + ["dN", "Inferred non-synonymous susbsitution rate"], + ["dN-dS", "Scaled by the length of the tested branches"], + ["P [dN/dS > 1]", "Binomial probability that S is no greater than the observed value, with Ps probability of success"], + ["P [dN/dS < 1]", "Binomial probability that S is no less than the observed value, with Ps probability of success"], + ["Total branch length", "The total length of branches contributing to inference at this site, and used to scale dN-dS"] + ] + }, + "analysis":{ + "authors":"Sergei L Kosakovsky Pond and Simon DW Frost", + "citation":"Not So Different After All: A Comparison of Methods for Detecting Amino Acid Sites Under Selection (2005). _Mol Biol Evol_ 22 (5): 1208-1222", + "contact":"spond@temple.edu", + "info":"SLAC (Single Likelihood Ancestor Counting)\n uses a maximum likelihood ancestral state reconstruction\n and minimum path substitution counting to estimate site - level\n dS and dN,\n and applies a simple binomial - based test to test\n if dS differs drom dN.\n The estimates aggregate information over all branches,\n so the signal is derived from\n pervasive diversification or conservation. A subset of branches can be selected\n for testing as well.\n Multiple partitions within a NEXUS file are also supported\n for recombination - aware analysis.\n ", + "requirements":"in-frame codon alignment and a phylogenetic tree", + "version":"2.00" + }, + "branch attributes":{ + "0":{ + "Node20":{ + "Global MG94xREV":0.001731141176898499, + "Nucleotide GTR":0.001684521619549293, + "amino-acid": [ +["A", "I", "A", "S", "E", "F", "S", "S", "L", "P", "S", "Y", "A", "A", "F", "A", "T", "A", "Q", "E", "A", "Y", "E", "Q", "A", "V", "A", "N", "G", "D", "S", "E", "V", "V", "L", "K", "N", "L", "K", "K", "S", "L", "N", "V", "A", "K", "S", "E", "F", "D", "R", "D", "A", "A", "M", "Q", "R", "K", "L", "E", "K", "M", "A", "D", "Q", "A", "M", "T", "Q", "M", "Y", "K", "Q", "A", "R", "S", "E", "D", "K", "R", "A", "K", "V", "T", "S", "A", "M", "Q", "T", "M", "L", "F", "T", "M", "L", "R", "K", "L", "D", "N", "D", "A", "L", "N", "N", "I", "I", "N", "N", "A", "R", "D", "G", "C", "V", "P", "L", "N", "I", 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[0.02371882618448924] + ], + "Log Likelihood":-1206.275362361884, + "Rate Distributions":{ + "non-synonymous/synonymous rate ratio for *test*": [ +[0.5481493272781195, 1] + ] + }, + "display order":1, + "estimated parameters":50 + }, + "Nucleotide GTR":{ + "AIC-c":2633.0046471406, + "Equilibrium frequencies": [ +[0.3251262626262627], + [0.1799242424242424], + [0.2026515151515151], + [0.2922979797979798] + ], + "Log Likelihood":-1247.247280799152, + "Rate Distributions":{ + "Substitution rate from nucleotide A to nucleotide C":0, + "Substitution rate from nucleotide A to nucleotide G":1, + "Substitution rate from nucleotide A to nucleotide T":0.3101631549852981, + "Substitution rate from nucleotide C to nucleotide G":1.129990583516242, + "Substitution rate from nucleotide C to nucleotide T":2.723444388603395, + "Substitution rate from nucleotide G to nucleotide T":1.720896006888861 + }, + "display order":0, + "estimated parameters":69 + } + }, + "input":{ + "file name":"/home/aglucaci/SARS-CoV-2/clades/B-1-617/nsp8.combined.fas", + "number of sequences":32, + "number of sites":198, + "partition count":1, + "trees":{ + "0":"(REFERENCE,(gb_MT226610_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_CHN_KMS1_2020_Segment_null_Host_Human,epi_isl_1589870_hCoV_19_India_WB_1931501009078_2021)Node20,gb_MT326179_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_UW_1572_2020_Segment_null_Host_Human,epi_isl_1589885_hCoV_19_India_WB_1931300250528_2021,(epi_isl_1615709_hCoV_19_England_CAMC_14E792B_2021,gb_MW523870_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_LA_CDC_STM_A100279_2021_Segment_null_Host_Human)Node4,epi_isl_1592421_hCoV_19_USA_MA_CDC_STM_000044850_2021,gb_MW345265_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0448_2020_Segment_null_Host_Human,gb_MW525063_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MI_CDC_STM_0000013_D10_2021_Segment_null_Host_Human,epi_isl_1181694_hCoV_19_USA_DE_DHSS_B1064373_2021,gb_MW585851_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_GA_CDC_STM_000004152_2021_Segment_null_Host_Human,(gb_MW583322_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_AL_CDC_STM_000001665_2021_Segment_null_Host_Human,gb_MW562702_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2102128070_2020_Segment_null_Host_Human,epi_isl_1384851_hCoV_19_India_MH_NCCS_ND13683_2021)Node38,epi_isl_1357692_hCoV_19_India_WB_1931500870015_2021,gb_MW486334_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_UW_2535_2020_Segment_null_Host_Human,epi_isl_1533793_hCoV_19_India_MH_NCCS_CHN21027888_2021,gb_LR757997_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_UNKNOWN_LR757997_Segment_null_Host_Human,epi_isl_1415270_hCoV_19_India_MH_NCCS_BJ2_2021,epi_isl_1543980_hCoV_19_Singapore_490_2021,epi_isl_1632256_hCoV_19_England_RAND_14E1D70_2021,gb_MT745751_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_DNAS_isl_BRB_2020_Segment_null_Host_Human,epi_isl_1573247_hCoV_19_Germany_un_RKI_I_068985_2021,gb_MW585867_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_000003621_2021_Segment_null_Host_Human,gb_MW540189_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01215_2020_Segment_null_Host_Human,epi_isl_1652118_hCoV_19_Singapore_575_2021,epi_isl_1652105_hCoV_19_Singapore_561_2021,gb_MW593074_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2645_2021_Segment_null_Host_Human,gb_MW154124_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC7567_2020_Segment_null_Host_Human,epi_isl_1416968_hCoV_19_Guadeloupe_IPP06229_2021,epi_isl_1544068_hCoV_19_India_MH_NCCS_RT231527_2021)" + } + }, + "tested":{ + "0":{ + "Node20":"test", + "Node38":"test", + "Node4":"test", + "REFERENCE":"test", + "epi_isl_1181694_hCoV_19_USA_DE_DHSS_B1064373_2021":"test", + "epi_isl_1357692_hCoV_19_India_WB_1931500870015_2021":"test", + "epi_isl_1384851_hCoV_19_India_MH_NCCS_ND13683_2021":"test", + "epi_isl_1415270_hCoV_19_India_MH_NCCS_BJ2_2021":"test", + "epi_isl_1416968_hCoV_19_Guadeloupe_IPP06229_2021":"test", + "epi_isl_1533793_hCoV_19_India_MH_NCCS_CHN21027888_2021":"test", + "epi_isl_1543980_hCoV_19_Singapore_490_2021":"test", + "epi_isl_1544068_hCoV_19_India_MH_NCCS_RT231527_2021":"test", + "epi_isl_1573247_hCoV_19_Germany_un_RKI_I_068985_2021":"test", + "epi_isl_1589870_hCoV_19_India_WB_1931501009078_2021":"test", + "epi_isl_1589885_hCoV_19_India_WB_1931300250528_2021":"test", + "epi_isl_1592421_hCoV_19_USA_MA_CDC_STM_000044850_2021":"test", + "epi_isl_1615709_hCoV_19_England_CAMC_14E792B_2021":"test", + "epi_isl_1632256_hCoV_19_England_RAND_14E1D70_2021":"test", + "epi_isl_1652105_hCoV_19_Singapore_561_2021":"test", + "epi_isl_1652118_hCoV_19_Singapore_575_2021":"test", + "gb_LR757997_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_UNKNOWN_LR757997_Segment_null_Host_Human":"test", + "gb_MT226610_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_CHN_KMS1_2020_Segment_null_Host_Human":"test", + "gb_MT326179_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_UW_1572_2020_Segment_null_Host_Human":"test", + "gb_MT745751_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_DNAS_isl_BRB_2020_Segment_null_Host_Human":"test", + "gb_MW154124_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC7567_2020_Segment_null_Host_Human":"test", + "gb_MW345265_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0448_2020_Segment_null_Host_Human":"test", + "gb_MW486334_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_UW_2535_2020_Segment_null_Host_Human":"test", + "gb_MW523870_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_LA_CDC_STM_A100279_2021_Segment_null_Host_Human":"test", + "gb_MW525063_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MI_CDC_STM_0000013_D10_2021_Segment_null_Host_Human":"test", + "gb_MW540189_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01215_2020_Segment_null_Host_Human":"test", + "gb_MW562702_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2102128070_2020_Segment_null_Host_Human":"test", + "gb_MW583322_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_AL_CDC_STM_000001665_2021_Segment_null_Host_Human":"test", + "gb_MW585851_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_GA_CDC_STM_000004152_2021_Segment_null_Host_Human":"test", + "gb_MW585867_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_000003621_2021_Segment_null_Host_Human":"test", + "gb_MW593074_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2645_2021_Segment_null_Host_Human":"test" + } + }, + "timers":{ + "Model fitting":{ + "order":1, + "timer":0 + }, + "Primary SLAC analysis":{ + "order":2, + "timer":1 + }, + "Total time":{ + "order":0, + "timer":1 + } + } +} \ No newline at end of file diff -r 5e8d0e777033 -r 60eec78ee26f test-data/summary/nsp8.combined.fas --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/nsp8.combined.fas Wed Jun 09 07:00:42 2021 +0000 @@ -0,0 +1,96 @@ +>epi_isl_1181694/hCoV-19/USA/DE-DHSS-B1064373/2021 +GCTATAGCCTCAGAGTTTAGTTCCCTTCCATCATATGCAGCTTTTGCTACTGCTCAAGAAGCTTATGAGCAGGCTGTTGCTAATGGTGATTCTGAAGTTGTTCTTAAAAAGTTGAAGAAGTCTTTGAATGTGGCTAAATCTGAATTTGACCGTGATGCAGCCATGCAACGTAAGTTGGAAAAGATGGCTGATCAAGCTATGACCCAAATGTATAAACAGGCTAGATCTGAGGACAAGAGGGCAAAAGTTACTAGTGCTATGCAGACAATGCTTTTCACTATGCTTAGAAAGTTGGATAATGATGCACTCAACAACATTATCAACAATGCAAGAGATGGTTGTGTTCCCTTGAACATAATACCTCTTACAACAGCAGCCAAACTAATGGTTGTCATACCAGACTATAACACATATAAAAATACGTGTGATGGTACAACATTTACTTATGCATCAGCATTGTGGGAAATCCAACAGGTTGTAGATGCAGATAGTAAAATTGTTCAACTTAGTGAAATTAGTATGGACAATTCACCTAATTTAGCATGGCCTCTTATTGTAACAGCTTTAAGGGCCAATTCTGCTGTCAAATTACAG + +>epi_isl_1357692/hCoV-19/India/WB-1931500870015/2021 +GCTATAGCCTCAGAGTTTAGTTCCCTTCCATCATATGCAGCTTTTGCTACTGCTCAAGAAGCTTATGAGCAGGCTGTTGCTAATGGTGATTCTGAAGTTGTTCTTAAAAAGTTGAAGAAGTCTTTGAATGTGGCTAAATCTGAATTTGACCGTGATGCAGCCATGCAACGTAAGTTGGAAAAGATGGCTGATCAAGCTATGACCCAAATGTATAAACAGGCTAGATCTGAGGACAAGAGGGCAAAAGTTACTAGTGCTATGCAGACAATGCTTTTCACTATGCTTAGAAAGTTGGATAATGATGCACTCAACAACATTATCAACAATGCAAGAGATGGTTGTGTTCCCTTGAACATAATACCTCTTACAACAGCAGCCAAACTAATGGTTGTCATACCAGACTATAACACATATAAAAATACGTGTGATGGTACAACATTTACTTATGCATCAGCATTGTGGGAAATCCAACAGGTTGTAGATGCAGATAGTAAAATTGTTCAACTTAGTGAAATTAGTATGGACAATTCACCTAATTTAGCATGGCCTCTTATTGTAACGGCTTTAAGGGCCAATTCTGCTGTCAAATTACAG + +>epi_isl_1384851/hCoV-19/India/MH-NCCS-ND13683/2021 +GCTATAGCCTCAGAGTTTAGTTCCCTTCCATCATATGCAGCTTTTGCTACTGCTCAAGAAGCTTATGAGCAGGCTGTTGCTAATGGTGATTCTGAAGTTGTTCTTAAAAAGTTGAAGAAGTCTTTGAATGTGGCTAAATCTGAATTTGACCGTGATGCAGCCATGCAACGTAAGTTGGAAAAGATGGCTGATCAAGCTATGACCCAAATGTATAAACAGGCTAGATCTGAGGACAAGAGGGCAAAAGTTACTAGTGCTATGCAGACAATGCTTTTCACTATGCTTAGAAAGTTGGATAATGATGCACTCAACAACATTATCAACAATGCAAGAGATGGTTGTGTTCCCTTGAACATAATACCTCTTACAACAGCAGCCAAATTAATGGTTGTCATACCAGACTATAACACATATAAAAATACGTGTGATGGTACAACATTTACTTATGCATCAGCATTGTGGGAAATCCAACAGGTTGTAGATGCAGATAGTAAAATTGTTCAACTTAGTGAAATTAGTATGGACAATTCACCTAATTTAGCATGGCCTCTTATTGTAACAGCTTTAAGGGCCAATTCTGCTGTCAAATTACAG + +>epi_isl_1415270/hCoV-19/India/MH-NCCS-BJ2/2021 +GCTATAGCCTCAGAGTTTAGTTCCCTTCCATCATATGCAGCTTTTGCTACTGCTCAAGAAGCTTATGAGCAGGCTGTTGCTAATGGTGATTCTGAAGTTGTTCTTAAAAAGTTGAAGAAGTCTTTGAATGTGGCTAAATCTGAATTTGACCGTGATGCAGCCATGCAACGTAAGTTGGAAAAGATGGCTGATCAAGCTGTGACCCAAATGTATAAACAGGCTAGATCTGAGGACAAGAGGGCAAAAGTTACTAGTGCTATGCAGACAATGCTTTTCACTATGCTTAGAAAGTTGGATAATGATGCACTCAACAACATTATCAACAATGCAAGAGATGGTTGTGTTCCCTTGAACATAATACCTCTTACAACAGCAGCCAAACTAATGGTTGTCATACCAGACTATAACACATATAAAAATACGTGTGATGGTACAACATTTACTTATGCATCAGCATTGTGGGAAATCCAACAGGTTGTAGATGCAGATAGTAAAATTGTTCAACTTAGTGAAATTAGTATGGACAATTCACCTAATTTAGCATGGCCTCTTATTGTAACAGCTTTAAGGGCCAATTCTGCTGTCAAATTACAG + +>epi_isl_1589870/hCoV-19/India/WB-1931501009078/2021 +GCTATAGCCTCAGAGTTTAGTTCCCTTCCATCATATGCAGCTTTTGCTACTGCTCAAGAAGCTTATGAGCAGGCTGTTGCTAATGGTGATTCTGAAGTTGTTCTTAAAAATTTGAAGAAGTCTTTGAATGTGGCTAAATCTGAATTTGACCGTGATGCAGCCATGCAACGTAAGTTGGAAAAGATGGCTGATCAAGCTATGACCCAAATGTATAAACAGGCTAGATCTGAGGACAAGAGGGCAAAAGTTACTAGTGCTATGCAGACAATGCTTTTCACTATGCTTAGAAAGTTGGATAATGATGCACTCAACAACATTATCAACAATGCAAGAGATGGTTGTGTTCCCTTGAACATAATACCTCTTACAACAGCAGCCAAACTAATGGTTGTCATACCAGACTATAACACATATAAAAATACGTGTGATGGTACAACATTTACTTATGCATCAGCATTGTGGGAAATCCAACAGGTTGTAGATGCAGATAGTAAAATTGTTCAACTTAGTGAAATTAGTATGGACAATTCACCTAATTTAGCATGGCCTCTTATTGTAACAGCTTTAAGGGCCAATTCTGCTGTCAAATTACAG + +>epi_isl_1589885/hCoV-19/India/WB-1931300250528/2021 +GCTATAGCCTCAGAGTTTAGTTCCCTTCCATCATATGCAGCTTTTGCTACTGCTCAAGAAGCTTATGAGCAGGCTGTTGCTAATGGTGATTCTGAAGTTGTTCTTAAAAAGTTGAAGAAGTCTTTGAATGTGGCTAAATCTGAATTTGACCGTGATGCAGCCATGCAACGTAAGTTGGAAAAGATGGCTGATCAAGCTATGACCCAAATGTATAAACAGGCTAGATCTGAGGACAAGAGGGCAAAAGTTACTAGTGCTATGCAGACAATGCTTTTCACTATGCTTAGAAAGTTGGATAATGATGCACTCAACAACATTATCAACAATGCAAGAGATGGTTGTGTTCCCTTGAACATAATACCTCTTATAACAGCAGCCAAACTAATGGTTGTCATACCAGACTATAACACATATAAAAATACGTGTGATGGTACAACATTTACTTATGCATCAGCATTGTGGGAAATCCAACAGGTTGTAGATGCAGATAGTAAAATTGTTCAACTTAGTGAAATTAGTATGGACAATTCACCTAATTTAGCATGGCCTCTTATTGTAACAGCTTTAAGGGCCAATTCTGCTGTCAAATTACAG + +>epi_isl_1592421/hCoV-19/USA/MA-CDC-STM-000044850/2021 +GCTATAGCCTCAGAGTTTAGTTCCCTTCCATCATATGCAGCTTTTGCTACTGCTCAAGAAGCTTATGAGCAGGCTGTTGCTAATGGTGATTCTGAAGTTGTTCTTAAAAAGTTGAAGAAGTCTTTGAATGTGGCTAAATCTGAATTTGACCGTGATGCAGCCATGCAACGTAAGTTGGAAAAGATGGCTGATCAAGCTATGACCCAAATGTATAAACAGGCTAGATCTGAGGACAAGAGGGCAAAAGTTACTAGTGCTATGCAGACAATGCTTTTCACTATGCTTAGAAAGTTGGATAATGATGCACTCAACAACATTATCAACAATGCAAGAGATGGTTGTGTTCCCTTGAACATAATACCTCTTACAACAGCAGCCAAACTAATGGTTGTCATACCAGACTATAACACATATAAAAATACGTGTGATGGTACAATATTTACTTATGCATCAGCATTGTGGGAAATCCAACAGGTTGTAGATGCAGATAGTAAAATTGTTCAACTTAGTGAAATTAGTATGGACAATTCACCTAATTTAGCATGGCCTCTTATTGTAACAGCTTTAAGGGCCAATTCTGCTGTCAAATTACAG + +>epi_isl_1615709/hCoV-19/England/CAMC-14E792B/2021 +GCTATAGCCTCAGAGTTTAGTTCCCTTCCATCATATGCAGCTTTTGCTACTGCTCAAGAAGCTTATGAGCAGGCTGTTGCTAATGGTGATTCTGAAGTTGTTCTTAAAAAGTTGAAGAAGTCTTTGAATGTGGCTAAATCTGAATTTGACCGTGATGCAGCCATGCAACGTAAGTTGGAAAAGATGGCTGATCAAGCTATGACCCAAATGTATAAACAGGCTAGATCTGAGGACAAGAGGGCAAAAGTTACTAGTGCTATGCAGACAATGCTTTTCACTATGCTTAGAAAGTTGGATAATGATGCACTCAACAACATTATCAACAATGCAAGAGATGGTTGTGTTCCCTTGAACATAATACCTCTTACAACAGCAGCCAAACTAATGGTTGTCATATCAGACTATAACACATATAAAAATACGTGTGATGGTACAACATTTACTTATGCATCAGCATTGTGGGAAATCCAACAGGTTGTAGATGCAGATAGTAAAATTGTTCAACTTAGTGAAATTAGTATGGACAATTCACCTAATTTAGCATGGCCTCTTATTGTAACAGCTTTAAGGGCCAATTCTGCTGTCAAATTACAG + +>epi_isl_1416968/hCoV-19/Guadeloupe/IPP06229/2021 +GCTATAGCCTCAGAGTTTAGTTCCTTTCCATCATATGCAGCTTTTGCTACTGCTCAAGAAGCTTATGAGCAGGCTGTTGCTAATGGTGATTCTGAAGTTGTTCTTAAAAAGTTGAAGAAGTCTTTGAATGTGGCTAAATCTGAATTTGACCGTGATGCAGCCATGCAACGTAAGTTGGAAAAGATGGCTGATCAAGCTATGACCCAAATGTATAAACAGGCTAGATCTGAGGACAAGAGGGCAAAAGTTACTAGTGCTATGCAGACAATGCTTTTCACTATGCTTAGAAAGTTGGATAATGATGCACTCAACAACATTATCAACAATGCAAGAGATGGTTGTGTTCCCTTGAACATAATACCTCTTACAACAGCAGCCAAACTAATGGTTGTCATACCAGACTATAACACATATAAAAATACGTGTGATGGTACAACATTTACTTATGCATCAGCATTGTGGGAAATCCAACAGGTTGTAGATGCAGATAGTAAAATTGTTCAACTTAGTGAAATTAGTATGGACAATTCACCTAATTTAGCATGGCCTCTTATTGTAACAGCTTTAAGGGCCAATTCTGCTGTCAAATTACAG + +>epi_isl_1533793/hCoV-19/India/MH-NCCS-CHN21027888/2021 +GCTATAGCCTCAGAGTTTAGTTCCCTTCCATCATATGCAGCTTTTGCTACTGCTCAAGAAGCTTATGAGCAGGCTGTTGCTAATGGTGACTCTGAAGTTGTTCTTAAAAAGTTGAAGAAGTCTTTGAATGTGGCTAAATCTGAATTTGACCGTGATGCAGCCATGCAACGTAAGTTGGAAAAGATGGCTGATCAAGCTATGACCCAAATGTATAAACAGGCTAGATCTGAGGACAAGAGGGCAAAAGTTACTAGTGCTATGCAGACAATGCTTTTCACTATGCTTAGAAAGTTGGATAATGATGCACTCAACAACATTATCAACAATGCAAGAGATGGTTGTGTTCCCTTGAACATAATACCTCTTACAACAGCAGCCAAACTAATGGTTGTCATACCAGACTATAACACATATAAAAATACGTGTGATGGTACAACATTTACTTATGCATCAGCATTGTGGGAAATCCAACAGGTTGTAGATGCAGATAGTAAAATTGTTCAACTTAGTGAAATTAGTATGGACAATTCACCTAATTTAGCATGGCCTCTTATTGTAACAGCTTTAAGGGCCAATTCTGCTGTCAAATTACAG + +>epi_isl_1543980/hCoV-19/Singapore/490/2021 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+GCTATAGCCTCAGAGTTTAGTTCCCTTCCATCATATGCAGCTTTTGCTACTGCTCAAGAAGCTTATGAGCAGGCTGTTGCTAATGGTGATTCTGAAGTTGTTCTTAAAAAGTTGAAGAAGTCTTTGAATGTGGCTAAATCTGAATTTGACCGTGATGCAGCCATGCAACGTAAGTTGGAAAAGATGGCTGATCAAGCTATGACCCAAATGTATAAACAGGCTAGATCTGAGGACAAGAGGGCAAAAGTTACTAGTGCTATGCAGACAATGCTTTTCACTATGCTTAGAAAGTTGGATAATGATGCACTTAACAACATTATCAACAATGCAAGAGATGGTTGTGTTCCCTTGAACATAATACCTCTTACAACAGCAGCCAAACTAATGGTTGTCATACCAGACTATAACACATATAAAAATACGTGTGATGGTACAACATTTACTTATGCATCAGCATTGTGGGAAATCCAACAGGTTGTAGATGCAGATAGTAAAATTGTTCAACTTAGTGAAATTAGTATGGACAATTCACCTAATTTAGCATGGCCTCTTATTGTAACAGCTTTAAGGGCCAATTCTGCTGTCAAATTACAG + +>epi_isl_1573247/hCoV-19/Germany/un-RKI-I-068985/2021 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Bayesian graphical models (2008). _Bioinformatics_ 24(17): 1949-1950", + "contact":"apoon42@uwo.ca", + "info":"BGM (Bayesian Graphical Model) uses a maximum likelihood ancestral state reconstruction to\nmap substitution (non-synonymous only for coding data) events to branches in the\nphylogeny and then analyzes the joint distribution of the\nsubstitution map using a Bayesian graphical model (network).\nNext, a Markov chain Monte Carlo analysis is used to generate\na random sample of network structures from the posterior\ndistribution given the data. Each node in the network\nrepresents a codon site in the alignment, and links (edges)\nbetween nodes indicate high posterior support for correlated\nsubstitutions at the two sites over time, which implies coevolution.", + "requirements":"in-frame codon alignment and a phylogenetic tree", + "version":"1.2" + }, + "branch attributes":{ + "0":{ + "Node10":{ + "models.codon.MG_REV.ModelDescription":0 + }, + "Node12":{ + "models.codon.MG_REV.ModelDescription":0 + }, + "Node13":{ + "models.codon.MG_REV.ModelDescription":0 + }, + "Node16":{ + "models.codon.MG_REV.ModelDescription":0 + }, + "Node19":{ + "models.codon.MG_REV.ModelDescription":0 + }, + "Node2":{ + "models.codon.MG_REV.ModelDescription":0 + }, + "Node20":{ + "models.codon.MG_REV.ModelDescription":0.001732564301319626 + }, + "Node23":{ + "models.codon.MG_REV.ModelDescription":0 + }, + "Node24":{ + "models.codon.MG_REV.ModelDescription":0 + }, + "Node27":{ + "models.codon.MG_REV.ModelDescription":0 + }, + "Node28":{ + 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