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annotate test-data/snpeff_stats.tabular @ 13:161f4383df15 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8ebda44b3ef25ef8ba030460134560547082289b
author iuc
date Sun, 20 Jan 2019 05:20:30 -0500
parents e0f4a651c6b9
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e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
diff changeset
1 Sample MODERATE splice_donor_variant+splice_region_variant+5_prime_UTR_variant+intron_variant_percent splice_region_variant+non_coding_exon_variant frameshift_variant+splice_acceptor_variant+splice_region_variant+splice_region_variant+intron_variant_percent frameshift_variant+splice_acceptor_variant+splice_donor_variant+splice_region_variant+splice_region_variant+splice_region_variant+intron_variant splice_donor_variant+splice_region_variant+5_prime_UTR_variant+intron_variant frameshift_variant+start_lost+splice_region_variant_percent NONE intragenic_variant_percent splice_region_variant+non_coding_exon_variant_percent UTR_3_PRIME splice_donor_variant+splice_region_variant+3_prime_UTR_variant+intron_variant_percent splice_acceptor_variant+splice_donor_variant+splice_region_variant+intron_variant+non_coding_exon_variant Ts_Tv_ratio splice_acceptor_variant+splice_donor_variant+splice_region_variant+splice_region_variant+splice_region_variant+intron_variant+non_coding_exon_variant_percent inframe_insertion+splice_region_variant_percent UTR_3_PRIME_percent inframe_deletion+splice_region_variant 5_prime_UTR_truncation+exon_loss_variant disruptive_inframe_deletion_percent INTRON LOW Het start_lost+disruptive_inframe_insertion frameshift_variant+splice_acceptor_variant+splice_donor_variant+splice_region_variant+splice_region_variant+splice_region_variant+intron_variant_percent inframe_deletion splice_acceptor_variant+splice_region_variant+3_prime_UTR_variant+intron_variant_percent non_coding_exon_variant frameshift_variant+stop_gained splice_acceptor_variant+splice_donor_variant+splice_region_variant+intron_variant+non_coding_exon_variant_percent DOWNSTREAM_percent disruptive_inframe_deletion+splice_region_variant MOTIF frameshift_variant+start_lost+splice_region_variant splice_donor_variant+splice_region_variant+splice_region_variant+intron_variant frameshift_variant+stop_gained_percent EXON splice_donor_variant+splice_region_variant+splice_region_variant+3_prime_UTR_variant+intron_variant upstream_gene_variant intron_variant_percent splice_donor_variant+splice_region_variant+splice_region_variant+3_prime_UTR_variant+intron_variant_percent inframe_deletion_percent HIGH_percent 3_prime_UTR_variant splice_donor_variant+intron_variant frameshift_variant+start_lost_percent disruptive_inframe_insertion non_coding_exon_variant_percent Change_rate 5_prime_UTR_truncation+exon_loss_variant_percent MODERATE_percent splice_acceptor_variant+splice_donor_variant+splice_region_variant+splice_region_variant+3_prime_UTR_variant+intron_variant_percent UTR_5_PRIME TRANSCRIPT frameshift_variant downstream_gene_variant MODIFIER_percent splice_acceptor_variant+inframe_deletion+splice_region_variant+splice_region_variant+intron_variant_percent LOW_percent frameshift_variant+splice_region_variant Missense_Silent_ratio Missing disruptive_inframe_deletion+splice_region_variant_percent splice_acceptor_variant+disruptive_inframe_deletion+splice_region_variant+splice_region_variant+intron_variant_percent frameshift_variant+stop_lost frameshift_variant+splice_acceptor_variant+splice_region_variant+intron_variant sequence_feature_percent intron_variant frameshift_variant+splice_region_variant_percent splice_acceptor_variant+splice_region_variant+splice_region_variant+intron_variant+non_coding_exon_variant splice_donor_variant+5_prime_UTR_variant+intron_variant Number_of_known_variants <br>(i.e. non-empty ID)_percent start_lost+disruptive_inframe_insertion_percent splice_acceptor_variant+splice_donor_variant+intron_variant Transitions DOWNSTREAM SPLICE_SITE_DONOR_percent frameshift_variant+stop_lost_percent splice_acceptor_variant+splice_region_variant+splice_region_variant+3_prime_UTR_variant+intron_variant_percent splice_acceptor_variant+splice_region_variant+intron_variant+non_coding_exon_variant_percent EXON_percent frameshift_variant_percent Number_of_variants_before_filter disruptive_inframe_insertion_percent splice_acceptor_variant+splice_donor_variant+splice_region_variant+splice_region_variant+intron_variant_percent splice_acceptor_variant+intron_variant stop_gained+inframe_insertion upstream_gene_variant_percent SPLICE_SITE_ACCEPTOR TF_binding_site_variant_percent SPLICE_SITE_REGION Genome_effective_length frameshift_variant+splice_acceptor_variant+splice_region_variant+intron_variant_percent splice_acceptor_variant+5_prime_UTR_variant+intron_variant INTERGENIC_percent splice_acceptor_variant+splice_donor_variant+splice_region_variant+splice_region_variant+splice_region_variant+intron_variant+non_coding_exon_variant 5_prime_UTR_variant UPSTREAM_percent splice_donor_variant+splice_region_variant+splice_region_variant+intron_variant+non_coding_exon_variant splice_acceptor_variant+disruptive_inframe_deletion+splice_region_variant+splice_region_variant+intron_variant splice_acceptor_variant+splice_region_variant+intron_variant 5_prime_UTR_variant_percent Type splice_acceptor_variant+inframe_deletion+splice_region_variant+splice_region_variant+intron_variant Hom splice_donor_variant+splice_region_variant+3_prime_UTR_variant+intron_variant splice_region_variant+splice_region_variant_percent UTR_5_PRIME_percent sequence_feature intergenic_region_percent transcript_percent HIGH frameshift_variant+splice_donor_variant+splice_region_variant+intron_variant UPSTREAM splice_acceptor_variant+splice_region_variant+splice_region_variant+intron_variant+non_coding_exon_variant_percent inframe_deletion+splice_region_variant_percent transcript splice_donor_variant+splice_region_variant+intron_variant+non_coding_exon_variant_percent Genome_total_length Number_of_effects NONE_percent frameshift_variant+splice_acceptor_variant+splice_region_variant+splice_region_variant+intron_variant SPLICE_SITE_ACCEPTOR_percent splice_acceptor_variant+intron_variant_percent splice_donor_variant+intron_variant_percent splice_donor_variant+5_prime_UTR_variant+intron_variant_percent splice_donor_variant+splice_region_variant+splice_region_variant+intron_variant+non_coding_exon_variant_percent splice_acceptor_variant+splice_donor_variant+intron_variant_percent splice_donor_variant+splice_region_variant+intron_variant splice_acceptor_variant+splice_region_variant+splice_region_variant+intron_variant_percent Transversions Genome disruptive_inframe_deletion MODIFIER splice_acceptor_variant+splice_region_variant+intron_variant_percent frameshift_variant+start_lost SPLICE_SITE_REGION_percent splice_acceptor_variant+splice_region_variant+intron_variant+non_coding_exon_variant INTRON_percent splice_acceptor_variant+5_prime_UTR_variant+intron_variant_percent splice_acceptor_variant+splice_region_variant+3_prime_UTR_variant+intron_variant TF_binding_site_variant MOTIF_percent frameshift_variant+splice_donor_variant+splice_region_variant+intron_variant_percent inframe_insertion splice_region_variant+intron_variant stop_gained+inframe_insertion_percent inframe_insertion+splice_region_variant Number_of_known_variants <br>(i.e. non-empty ID) splice_donor_variant+splice_region_variant+intron_variant+non_coding_exon_variant 3_prime_UTR_variant_percent splice_acceptor_variant+splice_region_variant+splice_region_variant+intron_variant splice_donor_variant+splice_region_variant+splice_region_variant+intron_variant_percent downstream_gene_variant_percent INTERGENIC splice_acceptor_variant+splice_region_variant+splice_region_variant+3_prime_UTR_variant+intron_variant splice_region_variant+splice_region_variant splice_donor_variant+splice_region_variant+intron_variant_percent splice_region_variant splice_acceptor_variant+splice_donor_variant+splice_region_variant+splice_region_variant+intron_variant splice_acceptor_variant+splice_donor_variant+splice_region_variant+splice_region_variant+3_prime_UTR_variant+intron_variant splice_region_variant+intron_variant_percent splice_region_variant_percent SPLICE_SITE_DONOR inframe_insertion_percent intergenic_region TRANSCRIPT_percent intragenic_variant
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
diff changeset
2 snpeff 3322.0 1.8e-05 462.0 0.000109 1.0 1.0 1.8e-05 2174772.0 0.004855 0.0084 15811.0 1.8e-05 2.0 0.0 9.1e-05 3.6e-05 0.287478 10.0 2.0 0.007418 2126738.0 2178258.0 524875.0 1.0 1.8e-05 159.0 0.000127 15320.0 21.0 3.6e-05 6.178119 2.0 986.0 1.0 3.0 0.000382 17369.0 1.0 354347.0 38.668709 1.8e-05 0.002891 0.024855 15811.0 41.0 0.000145 277.0 0.278551 3190.0 3.6e-05 0.060401 1.8e-05 3352.0 1.0 800.0 339790.0 60.30929 1.8e-05 39.605454 77.0 ? 0.0 3.6e-05 1.8e-05 3.0 2.0 39.535817 2126738.0 0.0014 13.0 2.0 78.616167 1.8e-05 61.0 0.0 339790.0 0.001473 5.5e-05 3.6e-05 9.1e-05 0.315806 0.014546 972155.0 0.005036 5.5e-05 224.0 3.0 6.442797 360.0 0.017928 5040.0 3101536026.0 3.6e-05 2.0 8.386471 5.0 3350.0 6.442797 12.0 1.0 32.0 0.06091 Count 1.0 392480.0 1.0 1.8e-05 0.060947 2174428.0 8.386471 0.0014 1367.0 3.0 354347.0 0.000236 0.000182 77.0 9.1e-05 32036512383.0 5499894.0 39.542071 6.0 0.006546 0.004073 0.000745 3.6e-05 0.000218 0.001109 15.0 1.8e-05 0.0 GRCh37.75 408.0 3316947.0 0.000582 8.0 0.091638 5.0 38.668709 3.6e-05 7.0 986.0 0.017928 5.5e-05 266.0 4390.0 5.5e-05 2.0 764271.0 5.0 0.287478 1.0 5.5e-05 6.178119 461247.0 2.0 1.0 0.000273 187.0 3.0 1.0 0.07982 0.0034 81.0 0.004836 461247.0 1.8e-05 267.0