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Change tool dependency to package_snpeff_3_2, now uses environment variable: SNPEFF_JAR_PATH for the location of snpeff jar files.
author Jim Johnson <jj@umn.edu>
date Wed, 18 Sep 2013 10:49:56 -0500
parents 192a236898f5
children
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1 ##fileformat=VCFv4.1
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2 ##samtoolsVersion=0.1.16 (r963:234)
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3 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
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4 ##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
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5 ##INFO=<ID=MQ,Number=1,Type=Integer,Description="Root-mean-square mapping quality of covering reads">
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6 ##INFO=<ID=FQ,Number=1,Type=Float,Description="Phred probability of all samples being the same">
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7 ##INFO=<ID=AF1,Number=1,Type=Float,Description="Max-likelihood estimate of the site allele frequency of the first ALT allele">
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8 ##INFO=<ID=G3,Number=3,Type=Float,Description="ML estimate of genotype frequencies">
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9 ##INFO=<ID=HWE,Number=1,Type=Float,Description="Chi^2 based HWE test P-value based on G3">
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10 ##INFO=<ID=CI95,Number=2,Type=Float,Description="Equal-tail Bayesian credible interval of the site allele frequency at the 95% level">
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11 ##INFO=<ID=PV4,Number=4,Type=Float,Description="P-values for strand bias, baseQ bias, mapQ bias and tail distance bias">
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12 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
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13 ##INFO=<ID=PC2,Number=2,Type=Integer,Description="Phred probability of the nonRef allele frequency in group1 samples being larger (,smaller) than in group2.">
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14 ##INFO=<ID=PCHI2,Number=1,Type=Float,Description="Posterior weighted chi^2 P-value for testing the association between group1 and group2 samples.">
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15 ##INFO=<ID=QCHI2,Number=1,Type=Integer,Description="Phred scaled PCHI2.">
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16 ##INFO=<ID=PR,Number=1,Type=Integer,Description="# permutations yielding a smaller PCHI2.">
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17 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
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18 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
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19 ##FORMAT=<ID=GL,Number=3,Type=Float,Description="Likelihoods for RR,RA,AA genotypes (R=ref,A=alt)">
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20 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="# high-quality bases">
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21 ##FORMAT=<ID=SP,Number=1,Type=Integer,Description="Phred-scaled strand bias P-value">
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22 ##FORMAT=<ID=PL,Number=-1,Type=Integer,Description="List of Phred-scaled genotype likelihoods, number of values is (#ALT+1)*(#ALT+2)/2">
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23 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT s_1_BcA2.sort.rmdup.Q20.noMh.bam
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24 NT_166464 696 . G C 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
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25 NT_166464 745 . G C 6.98 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:36,3,0:4
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26 NT_166464 7258 . A C 40 . DP=4;AF1=0.5008;CI95=0.5,0.5;DP4=1,0,2,1;MQ=32;FQ=-4.12;PV4=1,0.28,0.21,0.17 GT:PL:GQ 0/1:70,0,25:28
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27 NT_166464 7268 . A G 8.65 . DP=4;AF1=0.5004;CI95=0.5,0.5;DP4=1,0,1,1;MQ=30;FQ=3.32;PV4=1,0.017,0,1 GT:PL:GQ 0/1:38,0,28:32
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28 NT_166464 7283 . T C 11.3 . DP=3;AF1=0.501;CI95=0.5,0.5;DP4=1,0,1,1;MQ=30;FQ=-4.81;PV4=1,1,0,1 GT:PL:GQ 0/1:41,0,24:28
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29 NT_166464 7335 . G A 18.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=25;FQ=-33 GT:PL:GQ 1/1:50,6,0:10
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30 NT_166464 8030 . A G 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
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31 NT_166452 8268 . G A 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
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32 NT_166452 16693 . T C 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
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33 NT_166480 12474 . G A 6.2 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:35,3,0:4
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34 NT_166480 12483 . A G 4.77 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 0/1:33,3,0:3
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35 NT_166476 578 . C T 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
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36 NT_166476 22223 . A C 3.01 . DP=4;AF1=0.4998;CI95=0.5,0.5;DP4=0,2,2,0;MQ=32;FQ=4.63;PV4=0.33,0.26,0,0.42 GT:PL:GQ 0/1:30,0,43:28
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37 NT_166476 22256 . G A 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
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38 NT_166476 23076 . A T 8.44 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=25;FQ=-33 GT:PL:GQ 1/1:39,6,0:8
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39 NT_166476 23487 . C A 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
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40 NT_166454 64 . T A 8.64 . DP=7;AF1=0.5;CI95=0.5,0.5;DP4=1,4,2,0;MQ=29;FQ=11.3;PV4=0.14,1,1,1 GT:PL:GQ 0/1:38,0,91:40
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41 NT_166454 95 . T A 9.52 . DP=7;AF1=0.5;CI95=0.5,0.5;DP4=2,3,1,1;MQ=29;FQ=12.3;PV4=1,0.19,1,1 GT:PL:GQ 0/1:39,0,101:41
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42 NT_166454 1580 . T C 4.77 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 0/1:33,3,0:3
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43 NT_166454 7132 . A G 42.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-33 GT:PL:GQ 1/1:74,6,0:10
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44 NT_166454 7142 . T C 42.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-33 GT:PL:GQ 1/1:74,6,0:10
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45 NT_166454 7181 . C A 11.1 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-33 GT:PL:GQ 1/1:42,6,0:9
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46 NT_166454 11670 . C T 4.61 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=37;FQ=-33 GT:PL:GQ 1/1:34,6,0:5
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47 NT_166454 15049 . A T 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-33 GT:PL:GQ 1/1:45,6,0:10
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48 NT_166454 15052 . TA T 35.2 . INDEL;DP=2;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-40.5 GT:PL:GQ 1/1:74,6,0:10
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49 NT_166454 15373 . C G 30.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=37;FQ=-33 GT:PL:GQ 1/1:62,6,0:10
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50 NT_166454 15388 . C G 22.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=37;FQ=-33 GT:PL:GQ 1/1:54,6,0:10
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51 NT_166454 15440 . TA T 28.2 . INDEL;DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=37;FQ=-40.5 GT:PL:GQ 1/1:67,6,0:10
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52 NT_166454 18840 . C T 6.79 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=25;FQ=-33 GT:PL:GQ 1/1:37,6,0:7
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53 NT_166454 18863 . T C 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=25;FQ=-33 GT:PL:GQ 1/1:45,6,0:10
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54 NT_166454 18933 . C T 4.77 . DP=3;AF1=0.5003;CI95=0.5,0.5;DP4=1,0,2,0;MQ=30;FQ=-3.1;PV4=1,0.032,0,0.31 GT:PL:GQ 0/1:33,0,28:30
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55 NT_166454 21433 . G T 6.02 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-33 GT:PL:GQ 1/1:36,6,0:6
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56 NT_166454 21485 . TAAAAA TAAAA 17.5 . INDEL;DP=3;AF1=1;CI95=0.5,1;DP4=0,0,1,2;MQ=37;FQ=-43.5 GT:PL:GQ 1/1:57,9,0:15
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57 NT_166481 473 . A C 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
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58 NT_166481 476 . A T 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
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59 NT_166481 558 . G C 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
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60 NT_166481 9526 . T C 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
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61 NT_166481 10879 . T C 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
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62 NT_166481 17878 . T C 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
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63 NT_166481 20402 . A G 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
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64 NT_166481 20413 . G T 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
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65 NT_166459 13329 . T G 20.1 . DP=3;AF1=0.5013;CI95=0.5,0.5;DP4=1,0,1,1;MQ=37;FQ=-5.45;PV4=1,0.48,1,0.33 GT:PL:GQ 0/1:50,0,23:26
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66 NT_166459 21532 . T C 6.98 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:36,3,0:4
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67 NT_166473 10619 . T A 4.13 . DP=4;AF1=0.5003;CI95=0.5,0.5;DP4=1,0,0,3;MQ=28;FQ=-3.64;PV4=0.25,0.036,0,1 GT:PL:GQ 0/1:32,0,27:29
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68 NT_166473 10641 . A T 47.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,1,3;MQ=28;FQ=-39 GT:PL:GQ 1/1:80,12,0:21
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69 NT_166461 20175 . G A 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
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70 NT_166462 4505 . A G 6.2 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:35,3,0:4
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71 NT_166462 4585 . C T 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
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72 NT_166462 25794 . A C 7.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
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73 NT_166462 25801 . T G 22.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=37;FQ=-33 GT:PL:GQ 1/1:54,6,0:10
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74 NT_166462 25952 . T C 32.1 . DP=9;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=37;FQ=-45 GT:PL:GQ 1/1:65,18,0:33
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75 NT_166462 25967 . T C 135 . DP=9;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=37;FQ=-54 GT:PL:GQ 1/1:168,27,0:51
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76 NT_166462 26035 . T C 82 . DP=9;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=37;FQ=-54 GT:PL:GQ 1/1:115,27,0:51
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77 NT_166462 26537 . C G 83.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,1,3;MQ=37;FQ=-39 GT:PL:GQ 1/1:116,12,0:21
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78 NT_166462 26577 . A C 29.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,1,3;MQ=37;FQ=-39 GT:PL:GQ 1/1:62,12,0:21
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79 NT_166462 26682 . A G 222 . DP=19;AF1=1;CI95=1,1;DP4=0,0,9,9;MQ=30;FQ=-81 GT:PL:GQ 1/1:255,54,0:99
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80 NT_166462 26690 . A G 184 . DP=20;AF1=1;CI95=1,1;DP4=0,0,10,10;MQ=31;FQ=-87 GT:PL:GQ 1/1:217,60,0:99
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81 NT_166462 26717 . A G 207 . DP=10;AF1=1;CI95=1,1;DP4=0,0,6,4;MQ=36;FQ=-57 GT:PL:GQ 1/1:240,30,0:57
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
82 NT_166462 26722 . T C 98 . DP=10;AF1=1;CI95=1,1;DP4=0,0,6,4;MQ=36;FQ=-57 GT:PL:GQ 1/1:131,30,0:57
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
83 NT_166462 26762 . CAA CAAA 207 . INDEL;DP=10;AF1=1;CI95=1,1;DP4=0,0,6,4;MQ=36;FQ=-64.5 GT:PL:GQ 1/1:248,30,0:57
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
84 NT_166453 185 . A C 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
85 NT_166453 198 . T G 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
86 NT_166453 264 . T C 3.54 . DP=2;AF1=0.5;CI95=0.5,0.5;DP4=1,0,0,1;MQ=37;FQ=3.54;PV4=1,1,1,1 GT:PL:GQ 0/1:31,0,31:29
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
87 NT_166453 312 . A G 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
88 NT_166453 321 . C T 6.2 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:35,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
89 NT_166453 20370 . G C 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
90 NT_166467 12821 . C T 6.2 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:35,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
91 NT_166338 16706 . C A 4.77 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 0/1:33,3,0:3
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
92 NT_166338 16707 . T A 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
93 NT_166338 16708 . C G 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
94 NT_166338 16774 . G C 3.54 . DP=2;AF1=0.5;CI95=0.5,0.5;DP4=0,1,1,0;MQ=37;FQ=3.54;PV4=1,1,1,1 GT:PL:GQ 0/1:31,0,31:29
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
95 NT_166442 37512 . G A 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
96 NT_166442 37558 . A G 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
97 NT_166442 37567 . A G 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
98 NT_166451 487 . A G 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
99 NT_166450 27330 . T A 28 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=33;FQ=-36 GT:PL:GQ 1/1:60,9,0:16
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
100 NT_166450 27339 . T C 51 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=33;FQ=-36 GT:PL:GQ 1/1:83,9,0:16
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
101 NT_166450 27452 . G A 101 . DP=11;AF1=1;CI95=1,1;DP4=0,0,6,4;MQ=37;FQ=-57 GT:PL:GQ 1/1:134,30,0:57
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
102 NT_166450 27483 . T C 67.3 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,3,2;MQ=37;FQ=-42 GT:PL:GQ 1/1:100,15,0:27
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
103 NT_166450 27488 . T G 7.59 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=37;FQ=-33 GT:PL:GQ 1/1:38,6,0:7
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
104 NT_166450 27538 . A G 12 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=25;FQ=-33 GT:PL:GQ 1/1:43,6,0:9
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
105 NT_166450 27561 . T C 48.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,2,4;MQ=27;FQ=-45 GT:PL:GQ 1/1:81,18,0:33
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
106 NT_166450 27591 . T C 54.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,2,4;MQ=27;FQ=-45 GT:PL:GQ 1/1:87,18,0:33
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
107 NT_166450 27618 . T C 77.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,2,4;MQ=27;FQ=-45 GT:PL:GQ 1/1:110,18,0:33
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
108 NT_166450 27627 . A G 102 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,2,4;MQ=27;FQ=-45 GT:PL:GQ 1/1:135,18,0:33
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
109 NT_166450 27651 . G A 10.2 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-33 GT:PL:GQ 1/1:41,6,0:8
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
110 NT_166450 27659 . C A 65 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,1;MQ=37;FQ=-36 GT:PL:GQ 1/1:97,9,0:16
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
111 NT_166450 27664 . T C 31.5 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,3,1;MQ=37;FQ=-39 GT:PL:GQ 1/1:64,12,0:21
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
112 NT_166450 27700 . T C 106 . DP=8;AF1=1;CI95=1,1;DP4=0,0,5,3;MQ=37;FQ=-51 GT:PL:GQ 1/1:139,24,0:45
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
113 NT_166450 27798 . C T 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
114 NT_166450 27807 . T A 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
115 NT_166450 27813 . A C 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
116 NT_166447 29896 . A G 4.77 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 0/1:33,3,0:3
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
117 NT_166468 8984 . G C 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
118 NT_166468 8986 . G A 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
119 NT_166468 8989 . G T 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
120 NT_166477 2080 . T A 3.02 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 0/1:30,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
121 NT_166455 23979 . C A 6.98 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:36,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
122 NT_166291 4663 . G A 11.1 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-33 GT:PL:GQ 1/1:42,6,0:9
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
123 NT_166291 4684 . C G 32.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-33 GT:PL:GQ 1/1:64,6,0:10
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
124 NT_166291 27578 . G A 4.77 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 0/1:33,3,0:3
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
125 NT_166291 35549 . C G 117 . DP=10;AF1=1;CI95=1,1;DP4=0,0,6,4;MQ=36;FQ=-57 GT:PL:GQ 1/1:150,30,0:57
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
126 NT_166291 35756 . A G 198 . DP=20;AF1=1;CI95=1,1;DP4=0,0,9,10;MQ=37;FQ=-84 GT:PL:GQ 1/1:231,57,0:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
127 NT_166463 6735 . C A 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
128 NT_166463 6736 . T C 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
129 NT_166309 64876 . A G 25 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=33;FQ=-36 GT:PL:GQ 1/1:57,9,0:15
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
130 NT_166309 64910 . A C 30.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=30;FQ=-42 GT:PL:GQ 1/1:63,15,0:27
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
131 NT_166309 64925 . A G 29.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=30;FQ=-42 GT:PL:GQ 1/1:62,15,0:27
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
132 NT_166309 64960 . T G 45.5 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=28;FQ=-39 GT:PL:GQ 1/1:78,12,0:21
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
133 NT_166309 64971 . T G 30 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=25;FQ=-36 GT:PL:GQ 1/1:62,9,0:16
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
134 NT_166309 64979 . A C 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=25;FQ=-33 GT:PL:GQ 1/1:45,6,0:10
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
135 NT_166309 69760 . A G 52 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,1,2;MQ=33;FQ=-36 GT:PL:GQ 1/1:84,9,0:16
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
136 NT_166309 69765 . T C 42 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,1,2;MQ=33;FQ=-36 GT:PL:GQ 1/1:74,9,0:16
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
137 NT_166309 69773 . T C 35 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,1,2;MQ=33;FQ=-36 GT:PL:GQ 1/1:67,9,0:16
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
138 NT_166309 69799 . G C 25 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,1,2;MQ=33;FQ=-36 GT:PL:GQ 1/1:57,9,0:15
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
139 NT_166309 69869 . T C 35.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=37;FQ=-33 GT:PL:GQ 1/1:67,6,0:10
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
140 NT_166309 103113 . T A 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
141 NT_166309 139729 . G A 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
142 NT_166282 41545 . C T 3.02 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 0/1:30,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
143 NT_166282 94999 . C T 31.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,1,3;MQ=37;FQ=-39 GT:PL:GQ 1/1:64,12,0:21
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
144 NT_166282 95050 . T G 33 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,1,2;MQ=37;FQ=-36 GT:PL:GQ 1/1:65,9,0:16
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
145 NT_166314 112573 . C A 4.77 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 0/1:33,3,0:3
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
146 NT_166314 118593 . C T 35.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=34;FQ=-39 GT:PL:GQ 1/1:68,12,0:21
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
147 NT_166314 118608 . C T 73.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=34;FQ=-39 GT:PL:GQ 1/1:106,12,0:21
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
148 NT_166314 118836 . A C 84.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,1,3;MQ=37;FQ=-39 GT:PL:GQ 1/1:117,12,0:21
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
149 NT_166314 118924 . G C 212 . DP=10;AF1=1;CI95=1,1;DP4=0,0,3,7;MQ=37;FQ=-57 GT:PL:GQ 1/1:245,30,0:57
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
150 NT_166314 144387 . A T 3.54 . DP=2;AF1=0.5001;CI95=0.5,0.5;DP4=0,1,0,1;MQ=37;FQ=-3.07;PV4=1,1,1,1 GT:PL:GQ 0/1:31,0,29:29
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
151 NT_166314 155508 . A T 65.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,3,3;MQ=37;FQ=-45 GT:PL:GQ 1/1:98,18,0:33
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
152 NT_112000 52371 . G T 3.54 . DP=2;AF1=0.5;CI95=0.5,0.5;DP4=0,1,0,1;MQ=37;FQ=3.54;PV4=1,1,1,1 GT:PL:GQ 0/1:31,0,31:29
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
153 NT_112000 52375 . A C 3.54 . DP=2;AF1=0.5;CI95=0.5,0.5;DP4=0,1,0,1;MQ=37;FQ=3.54;PV4=1,1,1,1 GT:PL:GQ 0/1:31,0,31:29
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
154 NT_110857 19739 . A G 6.98 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:36,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
155 NT_166280 4649 . C A 3.54 . DP=2;AF1=0.5;CI95=0.5,0.5;DP4=1,0,0,1;MQ=37;FQ=3.54;PV4=1,1,1,1 GT:PL:GQ 0/1:31,0,31:29
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
156 NT_166280 137528 . T C 32.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=37;FQ=-33 GT:PL:GQ 1/1:64,6,0:10
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
157 NT_166280 137545 . C T 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=37;FQ=-33 GT:PL:GQ 1/1:45,6,0:10
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
158 NT_166311 1782 . C T 3.02 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 0/1:30,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
159 NT_166311 69821 . G A 65.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,4,1;MQ=33;FQ=-42 GT:PL:GQ 1/1:98,15,0:27
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
160 NT_166311 69841 . C A 42.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,4,1;MQ=33;FQ=-42 GT:PL:GQ 1/1:75,15,0:27
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
161 NT_166311 69894 . T G 26 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=37;FQ=-36 GT:PL:GQ 1/1:58,9,0:16
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
162 NT_166311 69917 . G A 20 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=37;FQ=-36 GT:PL:GQ 1/1:52,9,0:15
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
163 NT_166310 83175 . C G 3.55 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 0/1:31,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
164 NT_166438 13070 . C A 6.98 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:36,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
165 NT_162750 40051 . G A 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
166 NT_162750 40058 . A G 6.2 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:35,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
167 NT_162750 71153 . C G 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
168 NT_162750 71157 . T G 6.2 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:35,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
169 NT_166387 1835 . C G 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
170 NT_166281 28467 . A G 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
171 NT_166281 28468 . G A 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
172 NT_166313 178838 . G C 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
173 NT_166313 179067 . C T 3.01 . DP=2;AF1=0.4999;CI95=0.5,0.5;DP4=1,0,1,0;MQ=37;FQ=3.25;PV4=1,1,1,1 GT:PL:GQ 0/1:30,0,31:28
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
174 NT_166313 179084 . T C 3.54 . DP=2;AF1=0.5001;CI95=0.5,0.5;DP4=1,0,1,0;MQ=37;FQ=-3.07;PV4=1,1,1,1 GT:PL:GQ 0/1:31,0,29:29
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
175 NT_166313 179560 . A G 97 . DP=6;AF1=0.5032;CI95=0.5,0.5;DP4=1,0,1,4;MQ=35;FQ=-8.63;PV4=0.33,0.019,0.35,1 GT:PL:GQ 0/1:127,0,19:22
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
176 NT_166313 179573 . A T 76.1 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,2,4;MQ=35;FQ=-45 GT:PL:GQ 1/1:109,18,0:33
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
177 NT_166313 179575 . C T 68 . DP=7;AF1=0.5;CI95=0.5,0.5;DP4=1,1,1,4;MQ=36;FQ=26;PV4=1,0.0056,0.29,1 GT:PL:GQ 0/1:98,0,53:56
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
178 NT_166313 179587 . A G 42 . DP=8;AF1=0.5;CI95=0.5,0.5;DP4=1,2,1,4;MQ=36;FQ=42.9;PV4=1,0.0032,0.24,1 GT:PL:GQ 0/1:72,0,74:73
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
179 NT_166313 180199 . A G 64 . DP=13;AF1=0.5;CI95=0.5,0.5;DP4=9,0,3,1;MQ=37;FQ=67;PV4=0.31,1,1,1 GT:PL:GQ 0/1:94,0,143:97
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
180 NT_166313 180204 . C T 17.1 . DP=14;AF1=0.5;CI95=0.5,0.5;DP4=9,0,3,1;MQ=37;FQ=20.1;PV4=0.31,5.5e-06,1,1 GT:PL:GQ 0/1:47,0,143:50
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
181 NT_166313 180258 . C G 38 . DP=19;AF1=0.5;CI95=0.5,0.5;DP4=12,2,2,2;MQ=36;FQ=41;PV4=0.2,0.37,0.029,1 GT:PL:GQ 0/1:68,0,212:71
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
182 NT_166313 180274 . A G 45 . DP=14;AF1=0.5;CI95=0.5,0.5;DP4=5,0,3,6;MQ=36;FQ=47.6;PV4=0.031,2.3e-05,0.15,1 GT:PL:GQ 0/1:75,0,85:78
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
183 NT_166313 180300 . A T 11.3 . DP=15;AF1=0.5;CI95=0.5,0.5;DP4=4,6,1,4;MQ=36;FQ=14.2;PV4=0.6,1.7e-08,1,1 GT:PL:GQ 0/1:41,0,208:43
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
184 NT_166313 180331 . C T 189 . DP=17;AF1=0.5;CI95=0.5,0.5;DP4=1,3,6,6;MQ=34;FQ=59;PV4=0.58,0.16,0.068,1 GT:PL:GQ 0/1:219,0,86:89
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
185 NT_166313 180352 . C T 126 . DP=17;AF1=0.5;CI95=0.5,0.5;DP4=5,5,3,4;MQ=34;FQ=129;PV4=1,1,1,1 GT:PL:GQ 0/1:156,0,196:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
186 NT_166313 180384 . G A 93 . DP=16;AF1=0.5;CI95=0.5,0.5;DP4=2,4,6,4;MQ=34;FQ=95.9;PV4=0.61,3.3e-10,0.041,1 GT:PL:GQ 0/1:123,0,141:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
187 NT_166313 180748 . A C 18.1 . DP=7;AF1=0.5;CI95=0.5,0.5;DP4=4,1,2,0;MQ=37;FQ=21;PV4=1,1,1,0.13 GT:PL:GQ 0/1:48,0,123:51
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
188 NT_166313 180901 . A G 86.5 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,1,3;MQ=37;FQ=-39 GT:PL:GQ 1/1:119,12,0:21
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
189 NT_166313 182411 . T G 5.46 . DP=6;AF1=0.4999;CI95=0.5,0.5;DP4=3,0,0,3;MQ=35;FQ=7.8;PV4=0.1,0.0036,0.19,1 GT:PL:GQ 0/1:34,0,72:34
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
190 NT_166313 182447 . A G 10.4 . DP=5;AF1=0.5;CI95=0.5,0.5;DP4=2,0,0,3;MQ=35;FQ=13;PV4=0.1,0.014,0.25,0.14 GT:PL:GQ 0/1:40,0,53:42
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
191 NT_166313 183242 . C A 3.02 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 0/1:30,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
192 NT_166313 184154 . C A 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
193 NT_166313 184175 . G T 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
194 NT_166313 184807 . T C 15.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-33 GT:PL:GQ 1/1:47,6,0:10
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
195 NT_166313 184892 . T G 38.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-33 GT:PL:GQ 1/1:70,6,0:10
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
196 NT_166313 184925 . T C 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
197 NT_166313 184960 . T C 11.1 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=37;FQ=-33 GT:PL:GQ 1/1:42,6,0:9
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
198 NT_166313 184966 . C A 11.1 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=37;FQ=-33 GT:PL:GQ 1/1:42,6,0:9
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
199 NT_166313 185022 . C T 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=37;FQ=-33 GT:PL:GQ 1/1:40,6,0:8
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
200 NT_166313 185114 . G A 3.54 . DP=2;AF1=0.5;CI95=0.5,0.5;DP4=1,0,1,0;MQ=37;FQ=3.54;PV4=1,1,1,1 GT:PL:GQ 0/1:31,0,31:29
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
201 NT_166313 185707 . TGGGGGG TGGGG 53.4 . INDEL;DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,1;MQ=37;FQ=-43.5 GT:PL:GQ 1/1:93,9,0:16
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
202 NT_166313 186575 . T C 3.54 . DP=2;AF1=0.5;CI95=0.5,0.5;DP4=1,0,1,0;MQ=37;FQ=3.54;PV4=1,1,1,1 GT:PL:GQ 0/1:31,0,31:29
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
203 NT_166313 188906 . G C 3.02 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 0/1:30,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
204 NT_166313 189753 . T G 42 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,1;MQ=37;FQ=-36 GT:PL:GQ 1/1:74,9,0:16
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
205 NT_166313 189763 . G A 38 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,1;MQ=37;FQ=-36 GT:PL:GQ 1/1:70,9,0:16
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
206 NT_166313 190763 . A C 7.59 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=32;FQ=-33 GT:PL:GQ 1/1:38,6,0:7
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
207 NT_166313 190780 . T C 5.29 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=32;FQ=-33 GT:PL:GQ 1/1:35,6,0:6
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
208 NT_166313 191046 . C T 33.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=37;FQ=-33 GT:PL:GQ 1/1:65,6,0:10
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
209 NT_166313 191075 . C G 32.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=37;FQ=-33 GT:PL:GQ 1/1:64,6,0:10
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
210 NT_166313 206710 . CGAGAGAGAGAGAGAGAGA CGAGAGAGAGAGAGAGA 8.18 . INDEL;DP=8;AF1=0.5;CI95=0.5,0.5;DP4=4,2,2,0;MQ=37;FQ=10.8;PV4=1,1.5e-06,1,1 GT:PL:GQ 0/1:45,0,159:47
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
211 NT_166313 212911 . C T 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
212 NT_166313 242335 . A T 6.2 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:35,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
213 NT_166313 242381 . G C 3.54 . DP=3;AF1=0.5;CI95=0.5,0.5;DP4=1,0,0,1;MQ=37;FQ=3.54;PV4=1,1,1,1 GT:PL:GQ 0/1:31,0,31:29
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
214 NT_166313 243035 . G T 8.44 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=25;FQ=-33 GT:PL:GQ 1/1:39,6,0:8
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
215 NT_166313 243084 . A T 18.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=25;FQ=-33 GT:PL:GQ 1/1:50,6,0:10
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
216 NT_166313 243235 . T A 13.9 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=37;FQ=-33 GT:PL:GQ 1/1:45,6,0:10
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
217 NT_166313 243340 . C G 15.1 . DP=3;AF1=0.5008;CI95=0.5,0.5;DP4=1,0,2,0;MQ=37;FQ=-4.14;PV4=1,0.3,1,0.077 GT:PL:GQ 0/1:45,0,25:28
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
218 NT_161928 42786 . C T 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
219 NT_166378 24751 . T C 3.54 . DP=2;AF1=0.5;CI95=0.5,0.5;DP4=0,1,1,0;MQ=37;FQ=3.54;PV4=1,1,1,1 GT:PL:GQ 0/1:31,0,31:29
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
220 NT_166378 24753 . C T 3.54 . DP=2;AF1=0.5;CI95=0.5,0.5;DP4=0,1,1,0;MQ=37;FQ=3.54;PV4=1,1,1,1 GT:PL:GQ 0/1:31,0,31:29
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
221 NT_161926 91391 . C A 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
222 NT_161926 91392 . A G 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
223 NT_166385 319808 . G T 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
224 NT_165789 268949 . A G 130 . DP=11;AF1=1;CI95=1,1;DP4=0,0,5,5;MQ=33;FQ=-57 GT:PL:GQ 1/1:163,30,0:57
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
225 NT_165789 268956 . T G 133 . DP=11;AF1=1;CI95=1,1;DP4=0,0,5,5;MQ=33;FQ=-57 GT:PL:GQ 1/1:166,30,0:57
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
226 NT_165789 268973 . G A 102 . DP=8;AF1=1;CI95=1,1;DP4=0,0,4,4;MQ=32;FQ=-51 GT:PL:GQ 1/1:135,24,0:45
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
227 NT_165789 269002 . G A 47.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,1;MQ=25;FQ=-39 GT:PL:GQ 1/1:80,12,0:21
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
228 NT_165789 269016 . C T 38 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,1;MQ=25;FQ=-36 GT:PL:GQ 1/1:70,9,0:16
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
229 NT_165789 269124 . T A 53.2 . DP=9;AF1=0.5263;CI95=0.5,1;DP4=0,1,3,5;MQ=33;FQ=-17.1;PV4=1,5.2e-06,0.26,0.24 GT:PL:GQ 0/1:83,0,10:13
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
230 NT_165789 269148 . A G 9.53 . DP=5;AF1=0.5008;CI95=0.5,0.5;DP4=0,1,2,1;MQ=28;FQ=-4.22;PV4=1,0.0014,0,0.27 GT:PL:GQ 0/1:39,0,25:29
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
231 NT_165789 269163 . G T 7.8 . DP=3;AF1=0.5003;CI95=0.5,0.5;DP4=0,1,2,0;MQ=30;FQ=3.27;PV4=0.33,0.071,0,0.13 GT:PL:GQ 0/1:37,0,28:32
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
232 NT_165789 303609 . T G 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
233 NT_166361 150408 . G T 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
234 NT_166348 244139 . T G 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
235 NT_166348 244145 . G T 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
236 NT_166369 123725 . T C 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
237 NT_166417 80615 . C G 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
238 NT_166417 80639 . G A 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
239 NT_166383 378092 . T A 5.46 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:34,3,0:3
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
240 NT_166362 238907 . T G 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
241 NT_166362 238908 . A G 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
242 NT_165754 250017 . A G 190 . DP=22;AF1=1;CI95=1,1;DP4=0,0,11,8;MQ=37;FQ=-84 GT:PL:GQ 1/1:223,57,0:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
243 NT_165754 252055 . T A 3.54 . DP=2;AF1=0.5;CI95=0.5,0.5;DP4=1,0,0,1;MQ=37;FQ=3.54;PV4=1,1,1,1 GT:PL:GQ 0/1:31,0,31:29
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
244 NT_165754 293702 . G C 6.79 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=37;FQ=-33 GT:PL:GQ 1/1:37,6,0:7
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
245 NT_165754 300330 . C A 139 . DP=21;AF1=1;CI95=1,1;DP4=0,0,18,3;MQ=37;FQ=-90 GT:PL:GQ 1/1:172,63,0:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
246 NT_165754 300742 . AGG AGGG 3.8 . INDEL;DP=19;AF1=0.5;CI95=0.5,0.5;DP4=2,7,3,0;MQ=37;FQ=5.8;PV4=0.045,0.32,1,1 GT:PL:GQ 0/1:39,0,152:38
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
247 NT_165754 300745 . T G 10.4 . DP=19;AF1=0.5;CI95=0.5,0.5;DP4=0,7,5,0;MQ=35;FQ=13.2;PV4=0.0013,1.1e-06,0.038,1 GT:PL:GQ 0/1:40,0,128:42
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
248 NT_165754 304284 . T TC 12.7 . INDEL;DP=6;AF1=0.5;CI95=0.5,0.5;DP4=1,2,2,0;MQ=37;FQ=15.6;PV4=0.4,1,1,0.41 GT:PL:GQ 0/1:50,0,89:53
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
249 NT_165754 309950 . A T 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
250 NT_165754 311521 . A AT 6.36 . INDEL;DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=32;FQ=-40.5 GT:PL:GQ 1/1:44,6,0:7
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
251 NT_165754 329690 . N T 7.59 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=37;FQ=-33 GT:PL:GQ 1/1:38,6,0:7
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
252 NT_165754 329691 . N G 7.59 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=37;FQ=-33 GT:PL:GQ 1/1:38,6,0:7
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
253 NT_165754 329692 . N A 6.79 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=37;FQ=-33 GT:PL:GQ 1/1:37,6,0:7
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
254 NT_165754 329693 . N C 26 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=37;FQ=-36 GT:PL:GQ 1/1:58,9,0:16
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
255 NT_165754 338325 . G A 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
256 NT_161924 260016 . G A 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
257 NT_165795 433385 . G T 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
258 NT_166370 455714 . T G 4.77 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 0/1:33,3,0:3
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
259 NT_166424 307990 . T A 6.98 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:36,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
260 NT_161877 518452 . G C 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
261 NT_161877 518454 . A G 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
262 NT_166351 468564 . A T 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
263 NT_166408 488033 . C A 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
264 NT_166408 562716 . A G 6.98 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:36,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
265 NT_166349 214066 . A G 3.02 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 0/1:30,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
266 NT_166349 214070 . T G 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
267 NT_166391 47103 . C T 5.46 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:34,3,0:3
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
268 NT_165790 96824 . T G 6.2 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:35,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
269 NT_165790 96827 . A T 6.2 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:35,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
270 NT_166344 657504 . A C 6.2 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:35,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
271 NT_166371 140475 . C A 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
272 NT_166371 140477 . A C 3.55 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 0/1:31,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
273 NT_166371 140491 . C A 5.46 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:34,3,0:3
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
274 NT_161895 283625 . A T 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
275 NT_161895 744483 . C G 38 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=33;FQ=-36 GT:PL:GQ 1/1:70,9,0:16
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
276 NT_166404 51731 . A T 3.55 . DP=2;AF1=0.5004;CI95=0.5,0.5;DP4=0,1,1,0;MQ=37;FQ=-4.23;PV4=1,1,1,1 GT:PL:GQ 0/1:31,0,26:28
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
277 NT_161875 219900 . G A 6.2 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:35,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
278 NT_161875 219903 . T C 3.02 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 0/1:30,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
279 NT_161866 49262 . C G 6.2 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:35,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
280 NT_161866 49264 . A G 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
281 NT_161866 49265 . A G 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
282 NT_161872 293963 . C A 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
283 NT_161872 616242 . T A 4.77 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 0/1:33,3,0:3
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
284 NT_161872 714587 . C T 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
285 NT_161902 401831 . T C 6.98 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:36,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
286 NT_161902 923924 . G A 10.2 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=32;FQ=-33 GT:PL:GQ 1/1:41,6,0:8
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
287 NT_161937 232325 . A G 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
288 NT_161937 232331 . C A 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
289 NT_161937 310786 . G A 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
290 NT_161937 1343395 . C A 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
291 Y 356986 . A G 6.98 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:36,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
292 Y 362133 . G C 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
293 Y 372541 . G C 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
294 Y 385312 . A G 4.61 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=37;FQ=-33 GT:PL:GQ 1/1:34,6,0:5
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
295 Y 385313 . A G 4.61 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=37;FQ=-33 GT:PL:GQ 1/1:34,6,0:5
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
296 Y 472032 . A G 3.55 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 0/1:31,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
297 Y 503298 . A G 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
298 Y 529936 . C A 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
299 Y 534673 . T C 6.2 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:35,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
300 Y 601401 . C CAG 24.5 . INDEL;DP=10;AF1=0.5;CI95=0.5,0.5;DP4=5,1,2,1;MQ=37;FQ=27.5;PV4=1,0.061,1,0.00024 GT:PL:GQ 0/1:62,0,144:65
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
301 Y 602418 . T TGC 21.3 . INDEL;DP=2;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-40.5 GT:PL:GQ 1/1:60,6,0:10
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
302 Y 1448653 . A T 3.02 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 0/1:30,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
303 Y 2564922 . C G 4.61 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=25;FQ=-33 GT:PL:GQ 1/1:34,6,0:5
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
304 Y 2564933 . A T 5.29 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=25;FQ=-33 GT:PL:GQ 1/1:35,6,0:6
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
305 Y 2564937 . T C 4.61 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=25;FQ=-33 GT:PL:GQ 1/1:34,6,0:5
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
306 Y 2884117 . T C 3.55 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 0/1:31,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
307 19 3205820 . G A 158 . DP=20;AF1=1;CI95=1,1;DP4=0,0,9,9;MQ=36;FQ=-81 GT:PL:GQ 1/1:191,54,0:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
308 19 3205836 . A G 220 . DP=36;AF1=1;CI95=1,1;DP4=0,0,20,14;MQ=37;FQ=-129 GT:PL:GQ 1/1:253,102,0:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
309 19 3205943 . G C 152 . DP=21;AF1=1;CI95=1,1;DP4=0,0,8,10;MQ=37;FQ=-81 GT:PL:GQ 1/1:185,54,0:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
310 19 3205957 . G C 80.1 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,2,4;MQ=37;FQ=-45 GT:PL:GQ 1/1:113,18,0:33
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
311 19 3205995 . T C 67 . DP=18;AF1=1;CI95=1,1;DP4=0,0,1,13;MQ=32;FQ=-69 GT:PL:GQ 1/1:100,42,0:81
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
312 19 3206052 . A G 120 . DP=12;AF1=1;CI95=1,1;DP4=0,0,3,7;MQ=34;FQ=-57 GT:PL:GQ 1/1:153,30,0:57
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
313 19 3206060 . T A 71.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,3,3;MQ=33;FQ=-45 GT:PL:GQ 1/1:104,18,0:33
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
314 19 3206638 . T G 55.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,4,1;MQ=25;FQ=-42 GT:PL:GQ 1/1:88,15,0:27
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
315 19 3206671 . T C 53.4 . DP=6;AF1=0.5554;CI95=0.5,1;DP4=1,0,4,1;MQ=25;FQ=-20;PV4=1,0.38,1,1 GT:PL:GQ 0/1:83,0,7:10
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
316 19 3206673 . T C 23 . DP=6;AF1=0.5;CI95=0.5,0.5;DP4=3,0,2,1;MQ=25;FQ=18.3;PV4=1,0.39,1,1 GT:PL:GQ 0/1:53,0,46:48
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
317 19 3206703 . G A 64.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,4,1;MQ=25;FQ=-42 GT:PL:GQ 1/1:97,15,0:27
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
318 19 3281904 . A G 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
319 19 3352482 . C A 32.5 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=34;FQ=-39 GT:PL:GQ 1/1:65,12,0:21
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
320 19 3356313 . AC ACC 39.5 . INDEL;DP=4;AF1=0.5016;CI95=0.5,0.5;DP4=1,0,0,3;MQ=37;FQ=-12.8;PV4=0.25,1,1,0.27 GT:PL:GQ 0/1:77,0,22:25
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
321 19 3362225 . A G 23 . DP=5;AF1=0.5016;CI95=0.5,0.5;DP4=1,0,4,0;MQ=35;FQ=-6.18;PV4=1,0.014,0.34,0.022 GT:PL:GQ 0/1:53,0,22:25
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
322 19 3365671 . AC A 3.81 . INDEL;DP=4;AF1=0.5004;CI95=0.5,0.5;DP4=0,1,1,1;MQ=37;FQ=-7.67;PV4=1,0.16,1,0.012 GT:PL:GQ 0/1:39,0,28:33
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
323 19 3369050 . G GA 9.71 . INDEL;DP=2;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-40.5 GT:PL:GQ 1/1:48,6,0:8
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
324 19 3371339 . G A 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
325 19 3375209 . A AT 54 . INDEL;DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=37;FQ=-46.5 GT:PL:GQ 1/1:94,12,0:21
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
326 19 3457052 . CT CTTT 4.42 . INDEL;DP=8;AF1=0.5;CI95=0.5,0.5;DP4=2,0,2,0;MQ=34;FQ=6.48;PV4=1,0.051,0.21,0.38 GT:PL:GQ 0/1:40,0,56:40
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
327 19 3462257 . T C 4.77 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 0/1:33,3,0:3
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
328 19 3490405 . T A 3.54 . DP=2;AF1=0.5;CI95=0.5,0.5;DP4=1,0,0,1;MQ=37;FQ=3.54;PV4=1,1,1,1 GT:PL:GQ 0/1:31,0,31:29
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
329 19 3490564 . C G 15.1 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=37;FQ=-36 GT:PL:GQ 1/1:47,9,0:14
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
330 19 3547993 . T C 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
331 19 3582830 . T A 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
332 19 3586482 . T G 58 . DP=12;AF1=0.5;CI95=0.5,0.5;DP4=2,0,7,1;MQ=34;FQ=12.3;PV4=1,0.00069,0.18,1 GT:PL:GQ 0/1:88,0,39:42
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
333 19 3586484 . A C 56 . DP=12;AF1=0.5001;CI95=0.5,0.5;DP4=2,0,7,1;MQ=34;FQ=9.53;PV4=1,0.0044,0.18,1 GT:PL:GQ 0/1:86,0,36:39
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
334 19 3591114 . CTGTG CTG 47.5 . INDEL;DP=5;AF1=0.5016;CI95=0.5,0.5;DP4=0,1,4,0;MQ=37;FQ=-12.8;PV4=0.2,0.12,1,0.25 GT:PL:GQ 0/1:85,0,22:25
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
335 19 3591123 . T G 11.3 . DP=3;AF1=0.5004;CI95=0.5,0.5;DP4=0,1,2,0;MQ=37;FQ=3.43;PV4=0.33,0,1,0.17 GT:PL:GQ 0/1:41,0,28:31
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
336 19 3591876 . C G 3.54 . DP=2;AF1=0.5;CI95=0.5,0.5;DP4=1,0,1,0;MQ=37;FQ=3.54;PV4=1,1,1,1 GT:PL:GQ 0/1:31,0,31:29
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
337 19 3596029 . GACACACACACACACA GACACACACACACA 15.6 . INDEL;DP=7;AF1=0.5;CI95=0.5,0.5;DP4=2,1,2,0;MQ=37;FQ=18.5;PV4=1,7.9e-05,1,1 GT:PL:GQ 0/1:53,0,90:56
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
338 19 3596048 . TCACACACACACACACA TCACACACACACACA 35.2 . INDEL;DP=7;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-40.5 GT:PL:GQ 1/1:74,6,0:10
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
339 19 3610237 . CG CGGG 28.2 . INDEL;DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=37;FQ=-40.5 GT:PL:GQ 1/1:67,6,0:10
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
340 19 3612197 . CGG CGGG 12.7 . INDEL;DP=3;AF1=0.5013;CI95=0.5,0.5;DP4=1,0,1,1;MQ=33;FQ=-11.8;PV4=1,0.43,0.33,0.33 GT:PL:GQ 0/1:50,0,23:26
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
341 19 3615652 . C G 7.8 . DP=5;AF1=0.5003;CI95=0.5,0.5;DP4=0,1,0,2;MQ=33;FQ=3.27;PV4=1,0.046,0.33,0.32 GT:PL:GQ 0/1:37,0,28:32
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
342 19 3621243 . A G 3.55 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 0/1:31,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
343 19 3647660 . C A 3.41 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=37;FQ=-33 GT:PL:GQ 1/1:32,6,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
344 19 3649602 . T G 41.5 . DP=9;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=32;FQ=-39 GT:PL:GQ 1/1:74,12,0:21
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
345 19 3649604 . C A 26 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=33;FQ=-36 GT:PL:GQ 1/1:58,9,0:16
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
346 19 3649607 . T G 31.5 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=32;FQ=-39 GT:PL:GQ 1/1:64,12,0:21
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
347 19 3673470 . G T 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
348 19 3682731 . T G 3.02 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 0/1:30,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
349 19 3784152 . A G 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
350 19 3817931 . A T 17.1 . DP=10;AF1=0.5;CI95=0.5,0.5;DP4=1,6,1,1;MQ=37;FQ=20.1;PV4=0.42,1,1,7.9e-09 GT:PL:GQ 0/1:47,0,150:50
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
351 19 3885854 . TT TTAT 8.18 . INDEL;DP=4;AF1=0.5;CI95=0.5,0.5;DP4=0,2,0,2;MQ=37;FQ=10.5;PV4=1,0.26,1,0.36 GT:PL:GQ 0/1:45,0,56:46
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
352 19 3897463 . C CA 23.5 . INDEL;DP=12;AF1=0.5;CI95=0.5,0.5;DP4=4,3,0,4;MQ=37;FQ=26.5;PV4=0.19,0.02,1,2.5e-05 GT:PL:GQ 0/1:61,0,178:64
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
353 19 3899540 . G A 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
354 19 3903173 . C T 3.01 . DP=13;AF1=0.4997;CI95=0.5,0.5;DP4=4,4,3,0;MQ=36;FQ=4.77;PV4=0.24,0.028,0.052,1 GT:PL:GQ 0/1:30,0,163:28
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
355 19 3903429 . CTA C 31.5 . INDEL;DP=11;AF1=0.5;CI95=0.5,0.5;DP4=4,2,3,0;MQ=37;FQ=34.5;PV4=0.5,1.4e-09,1,1 GT:PL:GQ 0/1:69,0,157:72
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
356 19 3903506 . G GCC 30.5 . INDEL;DP=7;AF1=0.5;CI95=0.5,0.5;DP4=1,2,0,3;MQ=35;FQ=33.4;PV4=1,1,0.19,1 GT:PL:GQ 0/1:68,0,87:71
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
357 19 3909282 . CTG CTGTG 22.5 . INDEL;DP=6;AF1=0.5004;CI95=0.5,0.5;DP4=0,1,1,1;MQ=37;FQ=-7.4;PV4=1,0.4,1,0.33 GT:PL:GQ 0/1:60,0,28:31
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
358 19 3909704 . A T 3.55 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 0/1:31,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
359 19 3909837 . T C 3.54 . DP=2;AF1=0.5;CI95=0.5,0.5;DP4=0,1,0,1;MQ=37;FQ=3.54;PV4=1,1,1,1 GT:PL:GQ 0/1:31,0,31:29
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
360 19 3937591 . G A 4.61 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=37;FQ=-33 GT:PL:GQ 1/1:34,6,0:5
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
361 19 3944020 . TA T 6.55 . INDEL;DP=3;AF1=0.5004;CI95=0.5,0.5;DP4=0,1,1,1;MQ=33;FQ=-7.51;PV4=1,0.28,0.33,0 GT:PL:GQ 0/1:43,0,28:33
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
362 19 3955855 . T G 3.02 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 0/1:30,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
363 19 4012679 . A T 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
364 19 4036683 . C CCAT 16.6 . INDEL;DP=5;AF1=0.5;CI95=0.5,0.5;DP4=2,1,1,1;MQ=37;FQ=19.5;PV4=1,0.12,1,0.04 GT:PL:GQ 0/1:54,0,90:57
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
365 19 4097507 . G GCC 45.5 . INDEL;DP=5;AF1=0.5032;CI95=0.5,0.5;DP4=1,0,4,0;MQ=35;FQ=-15.6;PV4=1,1,0.34,0.34 GT:PL:GQ 0/1:83,0,19:22
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
366 19 4097921 . AG A 16.6 . INDEL;DP=5;AF1=0.5;CI95=0.5,0.5;DP4=0,2,2,1;MQ=35;FQ=16;PV4=0.4,0.028,0.25,0.013 GT:PL:GQ 0/1:54,0,53:53
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
367 19 4103486 . GT GTCT 21.5 . INDEL;DP=6;AF1=0.5004;CI95=0.5,0.5;DP4=0,1,2,0;MQ=37;FQ=-7.4;PV4=0.33,0.41,1,0.016 GT:PL:GQ 0/1:59,0,28:31
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
368 19 4109610 . A G 3.54 . DP=2;AF1=0.5;CI95=0.5,0.5;DP4=1,0,1,0;MQ=37;FQ=3.54;PV4=1,1,1,1 GT:PL:GQ 0/1:31,0,31:29
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
369 19 4126040 . GCCCCC GCCCC 38.5 . INDEL;DP=9;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=37;FQ=-55.5 GT:PL:GQ 1/1:79,21,0:39
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
370 19 4128088 . T C 3.54 . DP=2;AF1=0.5;CI95=0.5,0.5;DP4=1,0,0,1;MQ=37;FQ=3.54;PV4=1,1,1,1 GT:PL:GQ 0/1:31,0,31:29
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
371 19 4150222 . T TG 16.6 . INDEL;DP=9;AF1=0.5;CI95=0.5,0.5;DP4=3,3,2,1;MQ=36;FQ=19.5;PV4=1,0.35,0.085,4e-05 GT:PL:GQ 0/1:54,0,140:57
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
372 19 4192878 . T TG 159 . INDEL;DP=17;AF1=1;CI95=0.5,1;DP4=0,1,9,3;MQ=37;FQ=-40.5;PV4=0.31,0.48,1,0.4 GT:PL:GQ 1/1:198,6,0:10
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
373 19 4192885 . T A 8.65 . DP=9;AF1=0.5008;CI95=0.5,0.5;DP4=0,1,3,0;MQ=37;FQ=-4.25;PV4=0.25,0.045,1,0.44 GT:PL:GQ 0/1:38,0,25:29
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
374 19 4193254 . T C 111 . DP=9;AF1=1;CI95=1,1;DP4=0,0,5,2;MQ=32;FQ=-48 GT:PL:GQ 1/1:144,21,0:39
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
375 19 4194973 . CT C 114 . INDEL;DP=14;AF1=0.5;CI95=0.5,0.5;DP4=4,2,3,3;MQ=37;FQ=113;PV4=1,2.2e-05,1,0.018 GT:PL:GQ 0/1:152,0,150:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
376 19 4218544 . GACACACACACACACACACACAC GACACACACACACACACACAC 20.5 . INDEL;DP=14;AF1=0.5;CI95=0.5,0.5;DP4=0,10,0,3;MQ=37;FQ=23.5;PV4=1,0.28,1,1 GT:PL:GQ 0/1:58,0,144:61
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
377 19 4265650 . A C 15.1 . DP=8;AF1=0.5002;CI95=0.5,0.5;DP4=1,1,0,3;MQ=35;FQ=5.35;PV4=0.4,1,0.25,1 GT:PL:GQ 0/1:45,0,31:34
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
378 19 4275479 . A G 3.54 . DP=2;AF1=0.5;CI95=0.5,0.5;DP4=0,1,0,1;MQ=37;FQ=3.54;PV4=1,1,1,1 GT:PL:GQ 0/1:31,0,31:29
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
379 19 4287266 . TG T 11.5 . INDEL;DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=32;FQ=-40.5 GT:PL:GQ 1/1:50,6,0:9
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
380 19 4288411 . C A 14.2 . DP=13;AF1=0.5;CI95=0.5,0.5;DP4=4,5,1,3;MQ=36;FQ=17.1;PV4=1,0.00097,1,1 GT:PL:GQ 0/1:44,0,185:47
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
381 19 4293399 . G A 3.01 . DP=2;AF1=0.4999;CI95=0.5,0.5;DP4=0,1,0,1;MQ=37;FQ=3.25;PV4=1,1,1,1 GT:PL:GQ 0/1:30,0,31:28
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
382 19 4293435 . T A 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
383 19 4319284 . G GCCA 39.4 . INDEL;DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=33;FQ=-43.5 GT:PL:GQ 1/1:79,9,0:16
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
384 19 4320148 . AT A 53.4 . INDEL;DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,1;MQ=33;FQ=-43.5 GT:PL:GQ 1/1:93,9,0:16
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
385 19 4328716 . C G 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
386 19 4356928 . T C 9.49 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=37;FQ=-36 GT:PL:GQ 1/1:41,9,0:12
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
387 19 4395270 . T C 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
388 19 4397535 . G A 3.55 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 0/1:31,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
389 19 4616344 . A G 31.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-33 GT:PL:GQ 1/1:63,6,0:10
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
390 19 4619199 . G GACA 28.2 . INDEL;DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=37;FQ=-40.5 GT:PL:GQ 1/1:67,6,0:10
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
391 19 4746969 . G GA 21.3 . INDEL;DP=2;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-40.5 GT:PL:GQ 1/1:60,6,0:10
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
392 19 4784161 . A G 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
393 19 4785570 . G C 7.8 . DP=3;AF1=0.5003;CI95=0.5,0.5;DP4=1,0,1,1;MQ=37;FQ=3.27;PV4=1,0.034,1,0.025 GT:PL:GQ 0/1:37,0,28:32
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
394 19 4799879 . T C 34.8 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-33 GT:PL:GQ 1/1:66,6,0:10
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
395 19 4888267 . A T 3.54 . DP=3;AF1=0.5;CI95=0.5,0.5;DP4=1,0,0,1;MQ=37;FQ=3.54;PV4=1,1,1,1 GT:PL:GQ 0/1:31,0,31:29
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
396 19 4918151 . CT CTT 17.3 . INDEL;DP=4;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-40.5 GT:PL:GQ 1/1:56,6,0:10
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
397 19 4923064 . CA C 16.6 . INDEL;DP=4;AF1=0.5008;CI95=0.5,0.5;DP4=0,1,1,2;MQ=34;FQ=-9.99;PV4=1,0.11,0.33,0.33 GT:PL:GQ 0/1:54,0,25:28
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
398 19 4964673 . G GGA 7.98 . INDEL;DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=32;FQ=-40.5 GT:PL:GQ 1/1:46,6,0:8
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
399 19 5045349 . G GT 11.8 . INDEL;DP=4;AF1=0.5008;CI95=0.5,0.5;DP4=1,0,1,1;MQ=37;FQ=-10;PV4=1,0.47,1,1 GT:PL:GQ 0/1:49,0,25:29
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
400 19 5046911 . G GA 35.2 . INDEL;DP=3;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-40.5 GT:PL:GQ 1/1:74,6,0:10
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
401 19 5048333 . A G 4.77 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 0/1:33,3,0:3
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
402 19 5081755 . G A 20 . DP=6;AF1=0.5;CI95=0.5,0.5;DP4=1,3,1,1;MQ=37;FQ=23;PV4=1,0.22,1,1 GT:PL:GQ 0/1:50,0,107:53
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
403 19 5111720 . C CAG 28.2 . INDEL;DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=37;FQ=-40.5 GT:PL:GQ 1/1:67,6,0:10
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
404 19 5113937 . TC TCC 21.3 . INDEL;DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=37;FQ=-40.5 GT:PL:GQ 1/1:60,6,0:10
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
405 19 5116885 . T A 3.01 . DP=2;AF1=0.4999;CI95=0.5,0.5;DP4=0,1,1,0;MQ=37;FQ=3.25;PV4=1,1,1,1 GT:PL:GQ 0/1:30,0,31:28
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
406 19 5140839 . T A 3.54 . DP=2;AF1=0.5;CI95=0.5,0.5;DP4=1,0,1,0;MQ=37;FQ=3.54;PV4=1,1,1,1 GT:PL:GQ 0/1:31,0,31:29
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
407 19 5142716 . T A 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
408 19 5152822 . T TC 77.5 . INDEL;DP=8;AF1=0.5064;CI95=0.5,0.5;DP4=1,0,6,0;MQ=37;FQ=-18.6;PV4=1,0.48,1,0.0022 GT:PL:GQ 0/1:115,0,16:19
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
409 19 5152825 . A C 3.02 . DP=6;AF1=0.5001;CI95=0.5,0.5;DP4=1,0,2,0;MQ=37;FQ=-3.6;PV4=1,0.057,1,0.052 GT:PL:GQ 0/1:30,0,28:28
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
410 19 5154577 . C A 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
411 19 5226915 . T C 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
412 19 5245293 . G A 5.46 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:34,3,0:3
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
413 19 5245305 . G A 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
414 19 5264850 . A G 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
415 19 5274427 . T C 3.01 . DP=54;AF1=0.4997;CI95=0.5,0.5;DP4=22,18,6,5;MQ=37;FQ=4.77;PV4=1,1e-18,1,1 GT:PL:GQ 0/1:30,0,255:28
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
416 19 5274978 . C CG 99.7 . INDEL;DP=10;AF1=1;CI95=0.5,1;DP4=0,0,4,1;MQ=37;FQ=-49.5 GT:PL:GQ 1/1:140,15,0:27
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
417 19 5275059 . C CA 30.2 . INDEL;DP=6;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-40.5 GT:PL:GQ 1/1:69,6,0:10
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
418 19 5279268 . C CTT 40.5 . INDEL;DP=5;AF1=0.5008;CI95=0.5,0.5;DP4=1,0,3,0;MQ=37;FQ=-9.98;PV4=1,0.46,1,0.0034 GT:PL:GQ 0/1:78,0,25:28
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
419 19 5279373 . GT GTCT 115 . INDEL;DP=11;AF1=0.5263;CI95=0.5,1;DP4=1,0,7,1;MQ=35;FQ=-24.5;PV4=1,1,0.31,0.44 GT:PL:GQ 0/1:152,0,10:13
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
420 19 5279469 . C CG 12.7 . INDEL;DP=6;AF1=0.5;CI95=0.5,0.5;DP4=1,1,0,3;MQ=35;FQ=13.9;PV4=0.4,0.027,0.25,0.25 GT:PL:GQ 0/1:50,0,53:51
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
421 19 5293078 . A G 3.02 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 0/1:30,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
422 19 5293322 . A G 22 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=37;FQ=-36 GT:PL:GQ 1/1:54,9,0:15
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
423 19 5299338 . T C 6.98 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:36,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
424 19 5324189 . A G 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
425 19 5324197 . C T 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
426 19 5324249 . G C 5.29 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=37;FQ=-33 GT:PL:GQ 1/1:35,6,0:6
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
427 19 5325094 . T C 12 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=32;FQ=-33 GT:PL:GQ 1/1:43,6,0:9
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
428 19 5325106 . A G 25.8 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=32;FQ=-33 GT:PL:GQ 1/1:57,6,0:10
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
429 19 5325161 . T C 75.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,2,4;MQ=35;FQ=-45 GT:PL:GQ 1/1:108,18,0:33
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
430 19 5334753 . G A 122 . DP=10;AF1=1;CI95=1,1;DP4=0,0,3,7;MQ=29;FQ=-57 GT:PL:GQ 1/1:155,30,0:57
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
431 19 5334800 . G C 101 . DP=9;AF1=1;CI95=1,1;DP4=0,0,2,7;MQ=28;FQ=-54 GT:PL:GQ 1/1:134,27,0:51
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
432 19 5334810 . T C 29 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,1,2;MQ=25;FQ=-36 GT:PL:GQ 1/1:61,9,0:16
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
433 19 5371182 . ATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT ATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 28.5 . INDEL;DP=11;AF1=0.5;CI95=0.5,0.5;DP4=1,4,0,3;MQ=37;FQ=31.5;PV4=1,0.24,1,0.4 GT:PL:GQ 0/1:66,0,107:69
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
434 19 5415628 . A G 58.2 . DP=5;AF1=0.5207;CI95=0.5,1;DP4=0,1,2,2;MQ=30;FQ=-16.1;PV4=1,1,0.14,1 GT:PL:GQ 0/1:88,0,11:14
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
435 19 5415652 . C G 19.1 . DP=5;AF1=0.5;CI95=0.5,0.5;DP4=0,2,1,2;MQ=33;FQ=16.7;PV4=1,0.0019,0.11,1 GT:PL:GQ 0/1:49,0,45:47
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
436 19 5415658 . A T 35 . DP=5;AF1=0.5;CI95=0.5,0.5;DP4=0,2,1,2;MQ=33;FQ=15.1;PV4=1,1,0.11,1 GT:PL:GQ 0/1:65,0,42:45
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
437 19 5415664 . G A 14.2 . DP=5;AF1=0.5;CI95=0.5,0.5;DP4=0,2,1,2;MQ=33;FQ=16.1;PV4=1,0.0034,0.11,1 GT:PL:GQ 0/1:44,0,50:46
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
438 19 5423558 . A AT 121 . INDEL;DP=15;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=37;FQ=-61.5 GT:PL:GQ 1/1:162,27,0:51
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
439 19 5424274 . GG GGAG 46.5 . INDEL;DP=12;AF1=0.5;CI95=0.5,0.5;DP4=2,3,4,1;MQ=37;FQ=49.5;PV4=0.52,0.014,1,1 GT:PL:GQ 0/1:84,0,134:87
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
440 19 5426086 . A C 14.2 . DP=33;AF1=0.5;CI95=0.5,0.5;DP4=15,2,0,9;MQ=37;FQ=17.1;PV4=1.8e-05,1.7e-09,1,1 GT:PL:GQ 0/1:44,0,212:47
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
441 19 5462528 . A AGG 45.4 . INDEL;DP=5;AF1=1;CI95=0.5,1;DP4=0,0,1,2;MQ=37;FQ=-43.5 GT:PL:GQ 1/1:85,9,0:16
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
442 19 5479300 . C A 3.54 . DP=2;AF1=0.5;CI95=0.5,0.5;DP4=0,1,0,1;MQ=37;FQ=3.54;PV4=1,1,1,1 GT:PL:GQ 0/1:31,0,31:29
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
443 19 5480150 . G A 7.59 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=32;FQ=-33 GT:PL:GQ 1/1:38,6,0:7
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
444 19 5533657 . C G 3.55 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 0/1:31,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
445 19 5535804 . C T 6.2 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:35,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
446 19 5580726 . C T 3.02 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 0/1:30,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
447 19 5640300 . CA C 77.5 . INDEL;DP=10;AF1=0.5;CI95=0.5,0.5;DP4=1,3,1,4;MQ=37;FQ=71;PV4=1,0.049,1,0.065 GT:PL:GQ 0/1:115,0,106:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
448 19 5642274 . A G 9.52 . DP=10;AF1=0.5;CI95=0.5,0.5;DP4=1,6,0,3;MQ=37;FQ=12.3;PV4=1,0.0039,1,0.22 GT:PL:GQ 0/1:39,0,152:41
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
449 19 5646794 . C CAA 4.42 . INDEL;DP=11;AF1=0.5;CI95=0.5,0.5;DP4=5,2,0,4;MQ=36;FQ=6.56;PV4=0.061,0.00082,0.1,4.2e-05 GT:PL:GQ 0/1:40,0,170:40
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
450 19 5652568 . T TTC 47.5 . INDEL;DP=13;AF1=0.5;CI95=0.5,0.5;DP4=5,1,4,0;MQ=37;FQ=50.5;PV4=1,0.33,1,0.035 GT:PL:GQ 0/1:85,0,142:88
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
451 19 5652874 . CT CTT 45.5 . INDEL;DP=8;AF1=0.5;CI95=0.5,0.5;DP4=0,3,4,0;MQ=36;FQ=34.3;PV4=0.029,0.31,0.22,1 GT:PL:GQ 0/1:83,0,69:72
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
452 19 5655793 . T TTTG 15.6 . INDEL;DP=5;AF1=0.5;CI95=0.5,0.5;DP4=2,1,2,0;MQ=37;FQ=18.5;PV4=1,0.031,1,0.0029 GT:PL:GQ 0/1:53,0,90:56
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
453 19 5671522 . C CT 8.18 . INDEL;DP=8;AF1=0.5;CI95=0.5,0.5;DP4=3,1,0,2;MQ=37;FQ=10.8;PV4=0.4,0.24,1,0.028 GT:PL:GQ 0/1:45,0,113:47
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
454 19 5673355 . C G 16.1 . DP=4;AF1=0.5;CI95=0.5,0.5;DP4=0,2,1,1;MQ=37;FQ=18.7;PV4=1,0.012,1,0.00027 GT:PL:GQ 0/1:46,0,56:48
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
455 19 5673587 . AGCT AGCTTGCT 15.6 . INDEL;DP=7;AF1=0.5;CI95=0.5,0.5;DP4=0,3,2,0;MQ=37;FQ=18.5;PV4=0.1,0.4,1,0.18 GT:PL:GQ 0/1:53,0,79:56
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
456 19 5700971 . GT G 13.7 . INDEL;DP=4;AF1=0.5;CI95=0.5,0.5;DP4=2,0,0,2;MQ=37;FQ=15.4;PV4=0.33,0.057,1,0.00094 GT:PL:GQ 0/1:51,0,56:53
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
457 19 5722189 . A T 15.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=37;FQ=-33 GT:PL:GQ 1/1:47,6,0:10
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
458 19 5747411 . A ATT 28.2 . INDEL;DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=37;FQ=-40.5 GT:PL:GQ 1/1:67,6,0:10
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
459 19 5751303 . G GAC 36.5 . INDEL;DP=8;AF1=0.5;CI95=0.5,0.5;DP4=3,1,3,0;MQ=37;FQ=39.5;PV4=1,1,1,0.0091 GT:PL:GQ 0/1:74,0,110:77
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
460 19 5765309 . C T 3.02 . DP=3;AF1=0.5001;CI95=0.5,0.5;DP4=1,0,0,2;MQ=37;FQ=-3.6;PV4=0.33,0.14,1,1 GT:PL:GQ 0/1:30,0,28:28
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
461 19 5766155 . T TCCC 5.8 . INDEL;DP=3;AF1=0.5004;CI95=0.5,0.5;DP4=1,0,0,2;MQ=37;FQ=-7.54;PV4=0.33,0.044,1,1 GT:PL:GQ 0/1:42,0,28:33
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
462 19 5802669 . CCT CCTCT 23.5 . INDEL;DP=11;AF1=0.5001;CI95=0.5,0.5;DP4=1,1,3,0;MQ=33;FQ=-3.84;PV4=0.4,1,0.11,1 GT:PL:GQ 0/1:61,0,33:36
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
463 19 5837235 . G A 3.54 . DP=2;AF1=0.5;CI95=0.5,0.5;DP4=0,1,1,0;MQ=37;FQ=3.54;PV4=1,1,1,1 GT:PL:GQ 0/1:31,0,31:29
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
464 19 5853932 . G A 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
465 19 5894371 . G T 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
466 19 5899740 . A G 3.54 . DP=2;AF1=0.5;CI95=0.5,0.5;DP4=1,0,0,1;MQ=37;FQ=3.54;PV4=1,1,1,1 GT:PL:GQ 0/1:31,0,31:29
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
467 19 5902359 . GT G 20.5 . INDEL;DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=33;FQ=-43.5 GT:PL:GQ 1/1:60,9,0:15
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
468 19 5905108 . G C 3.54 . DP=2;AF1=0.5002;CI95=0.5,0.5;DP4=0,1,1,0;MQ=37;FQ=-3.4;PV4=1,1,1,1 GT:PL:GQ 0/1:31,0,28:29
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
469 19 5951787 . C T 18 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=37;FQ=-36 GT:PL:GQ 1/1:50,9,0:15
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
470 19 5956115 . CT CTT 20.5 . INDEL;DP=4;AF1=0.501;CI95=0.5,0.5;DP4=0,1,1,1;MQ=37;FQ=-10.9;PV4=1,1,1,0.33 GT:PL:GQ 0/1:58,0,24:27
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
471 19 5956116 . TA T 20.5 . INDEL;DP=4;AF1=0.5004;CI95=0.5,0.5;DP4=0,1,1,1;MQ=37;FQ=-7.4;PV4=1,0.24,1,0.31 GT:PL:GQ 0/1:58,0,28:31
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
472 19 5988978 . AGG AGGGG 95 . INDEL;DP=5;AF1=1;CI95=0.5,1;DP4=0,0,2,2;MQ=37;FQ=-46.5 GT:PL:GQ 1/1:135,12,0:21
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
473 19 5990457 . G GC 48.5 . INDEL;DP=6;AF1=0.5;CI95=0.5,0.5;DP4=2,0,2,1;MQ=37;FQ=18.5;PV4=1,1,1,0.11 GT:PL:GQ 0/1:86,0,53:56
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
474 19 5992164 . A T 6.98 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:36,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
475 19 6011296 . CTT CTTT 89 . INDEL;DP=6;AF1=1;CI95=0.5,1;DP4=0,0,1,3;MQ=37;FQ=-46.5 GT:PL:GQ 1/1:129,12,0:21
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
476 19 6047971 . C T 141 . DP=14;AF1=0.5;CI95=0.5,0.5;DP4=3,3,2,6;MQ=37;FQ=114;PV4=0.58,0.44,1,1 GT:PL:GQ 0/1:171,0,141:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
477 19 6071701 . A T 8.64 . DP=10;AF1=0.5;CI95=0.5,0.5;DP4=3,1,3,0;MQ=36;FQ=11.3;PV4=1,0.12,1,1 GT:PL:GQ 0/1:38,0,89:40
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
478 19 6084061 . CT CTT 14.6 . INDEL;DP=7;AF1=0.5;CI95=0.5,0.5;DP4=1,1,2,0;MQ=37;FQ=16.4;PV4=1,1,1,0.21 GT:PL:GQ 0/1:52,0,57:54
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
479 19 6116433 . G T 3.01 . DP=2;AF1=0.4999;CI95=0.5,0.5;DP4=1,0,1,0;MQ=37;FQ=3.25;PV4=1,1,1,1 GT:PL:GQ 0/1:30,0,31:28
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
480 19 6152712 . A G 34 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,1;MQ=30;FQ=-36 GT:PL:GQ 1/1:66,9,0:16
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
481 19 6152741 . T C 191 . DP=12;AF1=1;CI95=1,1;DP4=0,0,8,3;MQ=34;FQ=-60 GT:PL:GQ 1/1:224,33,0:63
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
482 19 6152749 . T C 167 . DP=17;AF1=1;CI95=1,1;DP4=0,0,11,5;MQ=35;FQ=-75 GT:PL:GQ 1/1:200,48,0:93
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
483 19 6152890 . T C 100 . DP=7;AF1=1;CI95=1,1;DP4=0,0,3,4;MQ=37;FQ=-48 GT:PL:GQ 1/1:133,21,0:39
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
484 19 6152982 . G A 4.77 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 0/1:33,3,0:3
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
485 19 6153036 . C T 55.5 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,2,2;MQ=37;FQ=-39 GT:PL:GQ 1/1:88,12,0:21
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
486 19 6153077 . C T 222 . DP=20;AF1=1;CI95=1,1;DP4=0,0,9,11;MQ=37;FQ=-87 GT:PL:GQ 1/1:255,60,0:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
487 19 6153163 . T C 194 . DP=9;AF1=1;CI95=1,1;DP4=0,0,3,6;MQ=37;FQ=-54 GT:PL:GQ 1/1:227,27,0:51
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
488 19 6175510 . A G 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
489 19 6228939 . CA C 78 . INDEL;DP=4;AF1=1;CI95=0.5,1;DP4=0,0,1,3;MQ=34;FQ=-46.5 GT:PL:GQ 1/1:118,12,0:21
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
490 19 6230906 . C G 15.1 . DP=5;AF1=0.5008;CI95=0.5,0.5;DP4=1,0,0,3;MQ=37;FQ=-4.14;PV4=0.25,0.0037,1,0.1 GT:PL:GQ 0/1:45,0,25:28
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
491 19 6249082 . T C 3.54 . DP=2;AF1=0.5;CI95=0.5,0.5;DP4=0,1,0,1;MQ=37;FQ=3.54;PV4=1,1,1,1 GT:PL:GQ 0/1:31,0,31:29
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
492 19 6251864 . G GA 28.2 . INDEL;DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=37;FQ=-40.5 GT:PL:GQ 1/1:67,6,0:10
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
493 19 6280998 . T C 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
494 19 6288939 . C A 6.2 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:35,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
495 19 6289471 . A G 18.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-33 GT:PL:GQ 1/1:50,6,0:10
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
496 19 6293530 . C T 3.54 . DP=2;AF1=0.5;CI95=0.5,0.5;DP4=1,0,1,0;MQ=37;FQ=3.54;PV4=1,1,1,1 GT:PL:GQ 0/1:31,0,31:29
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
497 19 6294628 . T TCC 70 . INDEL;DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=37;FQ=-46.5 GT:PL:GQ 1/1:110,12,0:21
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
498 19 6313685 . A G 4.77 . DP=5;AF1=0.4999;CI95=0.5,0.5;DP4=1,1,1,1;MQ=37;FQ=6.98;PV4=1,0.00041,1,0.0011 GT:PL:GQ 0/1:33,0,62:33
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
499 19 6314781 . G C 44.1 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=32;FQ=-45 GT:PL:GQ 1/1:77,18,0:33
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
500 19 6316439 . G GA 11.7 . INDEL;DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,1;MQ=33;FQ=-43.5 GT:PL:GQ 1/1:51,9,0:13
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
501 19 6322372 . G GC 10.6 . INDEL;DP=5;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=37;FQ=-40.5 GT:PL:GQ 1/1:49,6,0:9
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
502 19 6355840 . C CAG 11.8 . INDEL;DP=5;AF1=0.5;CI95=0.5,0.5;DP4=2,1,2,0;MQ=37;FQ=14.6;PV4=1,1,1,0.45 GT:PL:GQ 0/1:49,0,85:51
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
503 19 6363411 . G A 6.98 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:36,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
504 19 6365792 . G GT 47.5 . INDEL;DP=16;AF1=0.5;CI95=0.5,0.5;DP4=6,3,4,1;MQ=37;FQ=50.5;PV4=1,0.08,1,0.055 GT:PL:GQ 0/1:85,0,201:88
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
505 19 6365797 . A C 4.13 . DP=14;AF1=0.4998;CI95=0.5,0.5;DP4=6,3,4,0;MQ=37;FQ=6.2;PV4=0.5,5.7e-06,1,0.1 GT:PL:GQ 0/1:32,0,196:31
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
506 19 6372298 . T C 18 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=33;FQ=-36 GT:PL:GQ 1/1:50,9,0:15
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
507 19 6372626 . G GCC 16.6 . INDEL;DP=8;AF1=0.5008;CI95=0.5,0.5;DP4=1,0,3,0;MQ=37;FQ=-9.99;PV4=1,0.061,1,0.0096 GT:PL:GQ 0/1:54,0,25:28
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
508 19 6374284 . G A 13.2 . DP=7;AF1=0.5016;CI95=0.5,0.5;DP4=0,1,3,1;MQ=33;FQ=-6.21;PV4=0.4,0.012,0.25,1 GT:PL:GQ 0/1:43,0,22:25
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
509 19 6374286 . A C 4.13 . DP=7;AF1=0.5006;CI95=0.5,0.5;DP4=0,1,3,0;MQ=34;FQ=-4.62;PV4=0.25,0.031,0.33,1 GT:PL:GQ 0/1:32,0,25:29
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
510 19 6386021 . T TGGC 11.8 . INDEL;DP=3;AF1=0.5004;CI95=0.5,0.5;DP4=1,0,0,2;MQ=33;FQ=-7.43;PV4=0.33,0.44,0.33,0.33 GT:PL:GQ 0/1:49,0,28:32
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
511 19 6390455 . C A 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
512 19 6502037 . T G 3.55 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 0/1:31,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
513 19 6592212 . A G 6.02 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=32;FQ=-33 GT:PL:GQ 1/1:36,6,0:6
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
514 19 6642108 . C T 6.2 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:35,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
515 19 6905075 . A AGC 7.98 . INDEL;DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=37;FQ=-40.5 GT:PL:GQ 1/1:46,6,0:8
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
516 19 6909201 . T C 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
517 19 6915048 . T G 5.29 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=37;FQ=-33 GT:PL:GQ 1/1:35,6,0:6
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
518 19 6981442 . CT CTT 56.7 . INDEL;DP=13;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=33;FQ=-49.5 GT:PL:GQ 1/1:97,15,0:27
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
519 19 6986843 . A AG 12.7 . INDEL;DP=5;AF1=0.5008;CI95=0.5,0.5;DP4=1,0,1,2;MQ=37;FQ=-10;PV4=1,0.13,1,0.33 GT:PL:GQ 0/1:50,0,25:28
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
520 19 6992893 . T C 26 . DP=6;AF1=0.5;CI95=0.5,0.5;DP4=2,2,1,1;MQ=37;FQ=29;PV4=1,0.27,1,0.42 GT:PL:GQ 0/1:56,0,118:59
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
521 19 7032496 . G A 20.8 . DP=6;AF1=0.6243;CI95=0.5,1;DP4=0,1,4,0;MQ=30;FQ=-23;PV4=0.2,1,0.14,0.037 GT:PL:GQ 0/1:50,0,4:7
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
522 19 7032498 . T C 19.1 . DP=5;AF1=0.501;CI95=0.5,0.5;DP4=0,1,3,0;MQ=28;FQ=-4.76;PV4=0.25,0.1,0,0.0026 GT:PL:GQ 0/1:49,0,24:27
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
523 19 7039010 . CT C 30.2 . INDEL;DP=4;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-40.5 GT:PL:GQ 1/1:69,6,0:10
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
524 19 7052925 . TCC TCCCC 11.8 . INDEL;DP=3;AF1=0.5004;CI95=0.5,0.5;DP4=1,0,2,0;MQ=33;FQ=-7.43;PV4=1,0.4,0.33,1 GT:PL:GQ 0/1:49,0,28:32
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
525 19 7053458 . CTT CTTT 10.8 . INDEL;DP=3;AF1=0.501;CI95=0.5,0.5;DP4=0,1,1,1;MQ=37;FQ=-10.9;PV4=1,0.17,1,0.024 GT:PL:GQ 0/1:48,0,24:28
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
526 19 7074272 . TA T 4.42 . INDEL;DP=5;AF1=0.5;CI95=0.5,0.5;DP4=1,2,2,0;MQ=37;FQ=6.56;PV4=0.4,1,1,0.099 GT:PL:GQ 0/1:40,0,90:40
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
527 19 7096313 . CT CTT 28.5 . INDEL;DP=6;AF1=0.5;CI95=0.5,0.5;DP4=1,1,2,1;MQ=37;FQ=20.2;PV4=1,0.26,1,0.06 GT:PL:GQ 0/1:66,0,55:58
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
528 19 7108797 . GT G 24.2 . INDEL;DP=5;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-40.5 GT:PL:GQ 1/1:63,6,0:10
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
529 19 7109279 . CT CTT 63 . INDEL;DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,1;MQ=34;FQ=-46.5 GT:PL:GQ 1/1:103,12,0:21
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
530 19 7273732 . G GC 50.5 . INDEL;DP=7;AF1=0.504;CI95=0.5,0.5;DP4=0,1,0,4;MQ=37;FQ=-16.6;PV4=1,1,1,0.0018 GT:PL:GQ 0/1:88,0,18:21
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
531 19 7273860 . ACCT ACCTCCT 33.5 . INDEL;DP=5;AF1=0.5;CI95=0.5,0.5;DP4=1,1,0,3;MQ=35;FQ=24.2;PV4=0.4,1,0.25,0.021 GT:PL:GQ 0/1:71,0,59:62
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
532 19 7322919 . G C 5.46 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:34,3,0:3
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
533 19 7351944 . T A 4.77 . DP=6;AF1=0.4999;CI95=0.5,0.5;DP4=1,1,2,0;MQ=37;FQ=6.98;PV4=1,0.1,1,0.18 GT:PL:GQ 0/1:33,0,61:33
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
534 19 7359479 . CT CTT 41.4 . INDEL;DP=5;AF1=1;CI95=0.5,1;DP4=0,0,1,2;MQ=37;FQ=-43.5 GT:PL:GQ 1/1:81,9,0:16
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
535 19 7361488 . T TC 8.83 . INDEL;DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=32;FQ=-40.5 GT:PL:GQ 1/1:47,6,0:8
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
536 19 7401873 . A T 3.54 . DP=2;AF1=0.5;CI95=0.5,0.5;DP4=0,1,0,1;MQ=37;FQ=3.54;PV4=1,1,1,1 GT:PL:GQ 0/1:31,0,31:29
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
537 19 7435993 . G A 3.01 . DP=2;AF1=0.4999;CI95=0.5,0.5;DP4=0,1,0,1;MQ=37;FQ=3.25;PV4=1,1,1,1 GT:PL:GQ 0/1:30,0,31:28
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
538 19 7446286 . G A 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
539 19 7450404 . G C 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
540 19 7451189 . G C 3.54 . DP=2;AF1=0.5;CI95=0.5,0.5;DP4=1,0,1,0;MQ=37;FQ=3.54;PV4=1,1,1,1 GT:PL:GQ 0/1:31,0,31:29
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
541 19 7459826 . T C 3.54 . DP=2;AF1=0.5001;CI95=0.5,0.5;DP4=1,0,0,1;MQ=37;FQ=3.25;PV4=1,1,1,1 GT:PL:GQ 0/1:31,0,30:29
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
542 19 7473416 . T C 212 . DP=12;AF1=1;CI95=1,1;DP4=0,0,4,6;MQ=37;FQ=-57 GT:PL:GQ 1/1:245,30,0:57
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
543 19 7533049 . A G 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
544 19 7559363 . G T 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
545 19 7596698 . G A 24 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=37;FQ=-36 GT:PL:GQ 1/1:56,9,0:15
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
546 19 7609641 . G T 49 . DP=25;AF1=0.5;CI95=0.5,0.5;DP4=7,3,0,10;MQ=37;FQ=52;PV4=0.0031,5.7e-05,1,0.46 GT:PL:GQ 0/1:79,0,183:82
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
547 19 7609735 . A G 60 . DP=28;AF1=0.5;CI95=0.5,0.5;DP4=11,5,5,6;MQ=37;FQ=63;PV4=0.26,2.6e-15,1,0.22 GT:PL:GQ 0/1:90,0,255:93
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
548 19 7609740 . A G 141 . DP=27;AF1=0.5;CI95=0.5,0.5;DP4=7,2,9,9;MQ=37;FQ=130;PV4=0.23,6.6e-13,1,1 GT:PL:GQ 0/1:171,0,157:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
549 19 7610022 . A G 68 . DP=22;AF1=0.5;CI95=0.5,0.5;DP4=6,8,3,5;MQ=37;FQ=71;PV4=1,0.013,1,1 GT:PL:GQ 0/1:98,0,225:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
550 19 7612605 . A G 79 . DP=43;AF1=0.5;CI95=0.5,0.5;DP4=9,19,6,7;MQ=37;FQ=82;PV4=0.49,5e-12,0.072,0.43 GT:PL:GQ 0/1:109,0,255:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
551 19 7672449 . T C 3.54 . DP=2;AF1=0.5001;CI95=0.5,0.5;DP4=1,0,1,0;MQ=37;FQ=3.25;PV4=1,1,1,1 GT:PL:GQ 0/1:31,0,30:29
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
552 19 7742879 . T C 155 . DP=13;AF1=1;CI95=1,1;DP4=0,0,3,10;MQ=37;FQ=-66 GT:PL:GQ 1/1:188,39,0:75
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
553 19 7742923 . T C 222 . DP=29;AF1=1;CI95=1,1;DP4=0,0,10,16;MQ=37;FQ=-105 GT:PL:GQ 1/1:255,78,0:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
554 19 7742993 . A G 222 . DP=39;AF1=1;CI95=1,1;DP4=0,0,24,14;MQ=37;FQ=-141 GT:PL:GQ 1/1:255,114,0:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
555 19 7743097 . G A 222 . DP=36;AF1=1;CI95=1,1;DP4=0,0,12,24;MQ=37;FQ=-135 GT:PL:GQ 1/1:255,108,0:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
556 19 7743265 . A G 143 . DP=17;AF1=1;CI95=1,1;DP4=0,0,8,6;MQ=37;FQ=-69 GT:PL:GQ 1/1:176,42,0:81
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
557 19 7743284 . A G 102 . DP=7;AF1=1;CI95=1,1;DP4=0,0,4,3;MQ=37;FQ=-48 GT:PL:GQ 1/1:135,21,0:39
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
558 19 8034536 . A G 42.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-33 GT:PL:GQ 1/1:74,6,0:10
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
559 19 8050872 . T G 87.1 . DP=7;AF1=1;CI95=1,1;DP4=0,0,2,5;MQ=25;FQ=-48 GT:PL:GQ 1/1:120,21,0:39
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
560 19 8050884 . T C 104 . DP=8;AF1=1;CI95=1,1;DP4=0,0,2,6;MQ=25;FQ=-51 GT:PL:GQ 1/1:137,24,0:45
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
561 19 8050914 . A G 70 . DP=11;AF1=1;CI95=1,1;DP4=0,0,2,9;MQ=29;FQ=-60 GT:PL:GQ 1/1:103,33,0:63
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
562 19 8050917 . G A 103 . DP=12;AF1=1;CI95=1,1;DP4=0,0,2,9;MQ=29;FQ=-60 GT:PL:GQ 1/1:136,33,0:63
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
563 19 8050932 . A G 110 . DP=13;AF1=1;CI95=1,1;DP4=0,0,3,10;MQ=30;FQ=-66 GT:PL:GQ 1/1:143,39,0:75
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
564 19 8050976 . G T 182 . DP=19;AF1=1;CI95=1,1;DP4=0,0,4,15;MQ=36;FQ=-84 GT:PL:GQ 1/1:215,57,0:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
565 19 8050985 . T TA 214 . INDEL;DP=20;AF1=1;CI95=1,1;DP4=0,0,4,16;MQ=37;FQ=-94.5 GT:PL:GQ 1/1:255,60,0:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
566 19 8050996 . T C 169 . DP=19;AF1=1;CI95=1,1;DP4=0,0,4,15;MQ=36;FQ=-84 GT:PL:GQ 1/1:202,57,0:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
567 19 8051050 . G A 103 . DP=19;AF1=1;CI95=1,1;DP4=0,0,6,12;MQ=35;FQ=-81 GT:PL:GQ 1/1:136,54,0:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
568 19 8051066 . G A 122 . DP=10;AF1=1;CI95=1,1;DP4=0,0,3,7;MQ=34;FQ=-57 GT:PL:GQ 1/1:155,30,0:57
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
569 19 8051084 . T C 46.5 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,3,1;MQ=28;FQ=-39 GT:PL:GQ 1/1:79,12,0:21
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
570 19 8051096 . A G 19 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=30;FQ=-36 GT:PL:GQ 1/1:51,9,0:15
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
571 19 8051106 . T G 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=25;FQ=-33 GT:PL:GQ 1/1:44,6,0:9
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
572 19 8051236 . G A 93.1 . DP=7;AF1=1;CI95=1,1;DP4=0,0,4,3;MQ=27;FQ=-48 GT:PL:GQ 1/1:126,21,0:39
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
573 19 8051264 . G A 52.1 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,4,2;MQ=25;FQ=-45 GT:PL:GQ 1/1:85,18,0:33
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
574 19 8051283 . T A 87.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,4,2;MQ=25;FQ=-45 GT:PL:GQ 1/1:120,18,0:33
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
575 19 8051315 . A G 80.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,4,2;MQ=25;FQ=-45 GT:PL:GQ 1/1:113,18,0:33
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
576 19 8051323 . C G 28 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,2,1;MQ=25;FQ=-36 GT:PL:GQ 1/1:60,9,0:16
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
577 19 8051467 . G A 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=25;FQ=-33 GT:PL:GQ 1/1:44,6,0:9
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
578 19 8051469 . C T 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=25;FQ=-33 GT:PL:GQ 1/1:40,6,0:8
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
579 19 8051498 . T A 147 . DP=11;AF1=1;CI95=1,1;DP4=0,0,4,7;MQ=26;FQ=-60 GT:PL:GQ 1/1:180,33,0:63
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
580 19 8051502 . C T 113 . DP=12;AF1=1;CI95=1,1;DP4=0,0,4,5;MQ=25;FQ=-54 GT:PL:GQ 1/1:146,27,0:51
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
581 19 8051544 . G A 112 . DP=14;AF1=1;CI95=1,1;DP4=0,0,3,10;MQ=29;FQ=-66 GT:PL:GQ 1/1:145,39,0:75
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
582 19 8051546 . T C 104 . DP=13;AF1=1;CI95=1,1;DP4=0,0,3,10;MQ=29;FQ=-66 GT:PL:GQ 1/1:137,39,0:75
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
583 19 8051574 . T C 192 . DP=13;AF1=1;CI95=1,1;DP4=0,0,3,10;MQ=29;FQ=-66 GT:PL:GQ 1/1:225,39,0:75
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
584 19 8051593 . T C 45.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=35;FQ=-42 GT:PL:GQ 1/1:78,15,0:27
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
585 19 8100673 . C G 3.54 . DP=2;AF1=0.5001;CI95=0.5,0.5;DP4=1,0,1,0;MQ=37;FQ=3.25;PV4=1,1,1,1 GT:PL:GQ 0/1:31,0,30:29
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
586 19 8326732 . GA G 45 . INDEL;DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=32;FQ=-46.5 GT:PL:GQ 1/1:85,12,0:21
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
587 19 8326738 . T A 12.3 . DP=10;AF1=0.5012;CI95=0.5,0.5;DP4=1,0,0,3;MQ=32;FQ=-5.48;PV4=0.25,0.09,0.21,1 GT:PL:GQ 0/1:42,0,23:26
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
588 19 8326742 . A C 77.1 . DP=16;AF1=1;CI95=0.5,1;DP4=0,0,2,4;MQ=32;FQ=-45 GT:PL:GQ 1/1:110,18,0:33
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
589 19 8347286 . A G 25 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,1;MQ=30;FQ=-36 GT:PL:GQ 1/1:57,9,0:15
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
590 19 8347289 . A C 41.5 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,2,2;MQ=32;FQ=-39 GT:PL:GQ 1/1:74,12,0:21
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
591 19 8347296 . T C 118 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,4,2;MQ=33;FQ=-45 GT:PL:GQ 1/1:151,18,0:33
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
592 19 8347384 . G GA 214 . INDEL;DP=29;AF1=1;CI95=1,1;DP4=0,0,23,6;MQ=37;FQ=-122 GT:PL:GQ 1/1:255,87,0:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
593 19 8347394 . T A 222 . DP=28;AF1=1;CI95=1,1;DP4=0,0,22,5;MQ=37;FQ=-108 GT:PL:GQ 1/1:255,81,0:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
594 19 8347399 . C G 167 . DP=27;AF1=1;CI95=1,1;DP4=0,0,20,5;MQ=37;FQ=-102 GT:PL:GQ 1/1:200,75,0:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
595 19 8347408 . C G 222 . DP=23;AF1=1;CI95=1,1;DP4=0,0,17,5;MQ=37;FQ=-93 GT:PL:GQ 1/1:255,66,0:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
596 19 8347594 . A G 78.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,3,3;MQ=25;FQ=-45 GT:PL:GQ 1/1:111,18,0:33
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
597 19 8347628 . A G 108 . DP=8;AF1=1;CI95=1,1;DP4=0,0,5,3;MQ=28;FQ=-51 GT:PL:GQ 1/1:141,24,0:45
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
598 19 8347638 . G T 99 . DP=8;AF1=1;CI95=1,1;DP4=0,0,5,3;MQ=28;FQ=-51 GT:PL:GQ 1/1:132,24,0:45
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
599 19 8347649 . T C 107 . DP=8;AF1=1;CI95=1,1;DP4=0,0,5,3;MQ=28;FQ=-51 GT:PL:GQ 1/1:140,24,0:45
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
600 19 8347659 . T C 106 . DP=8;AF1=1;CI95=1,1;DP4=0,0,5,3;MQ=28;FQ=-51 GT:PL:GQ 1/1:139,24,0:45
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
601 19 8347769 . T G 26 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,1,2;MQ=25;FQ=-36 GT:PL:GQ 1/1:58,9,0:16
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
602 19 8347801 . A G 150 . DP=8;AF1=1;CI95=1,1;DP4=0,0,4,4;MQ=30;FQ=-51 GT:PL:GQ 1/1:183,24,0:45
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
603 19 8347804 . A G 106 . DP=8;AF1=1;CI95=1,1;DP4=0,0,4,4;MQ=30;FQ=-51 GT:PL:GQ 1/1:139,24,0:45
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
604 19 8347809 . T C 79 . DP=8;AF1=1;CI95=1,1;DP4=0,0,4,4;MQ=30;FQ=-51 GT:PL:GQ 1/1:112,24,0:45
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
605 19 8347870 . T C 149 . DP=9;AF1=1;CI95=1,1;DP4=0,0,4,4;MQ=30;FQ=-51 GT:PL:GQ 1/1:182,24,0:45
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
606 19 8347993 . A C 78 . DP=13;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=25;FQ=-57 GT:PL:GQ 1/1:111,30,0:57
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
607 19 8348001 . T G 86 . DP=18;AF1=1;CI95=1,1;DP4=0,0,0,16;MQ=27;FQ=-75 GT:PL:GQ 1/1:119,48,0:93
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
608 19 8348026 . G A 121 . DP=26;AF1=1;CI95=1,1;DP4=0,0,2,24;MQ=31;FQ=-105 GT:PL:GQ 1/1:154,78,0:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
609 19 8348048 . A G 222 . DP=41;AF1=1;CI95=1,1;DP4=0,0,9,30;MQ=34;FQ=-144 GT:PL:GQ 1/1:255,117,0:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
610 19 8348080 . C T 167 . DP=46;AF1=1;CI95=1,1;DP4=0,0,20,26;MQ=35;FQ=-165 GT:PL:GQ 1/1:200,138,0:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
611 19 8348129 . G A 222 . DP=36;AF1=1;CI95=1,1;DP4=0,0,21,14;MQ=35;FQ=-132 GT:PL:GQ 1/1:255,105,0:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
612 19 8348158 . C A 138 . DP=18;AF1=1;CI95=1,1;DP4=0,0,12,3;MQ=32;FQ=-72 GT:PL:GQ 1/1:171,45,0:87
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
613 19 8348160 . T A 179 . DP=15;AF1=1;CI95=1,1;DP4=0,0,11,3;MQ=32;FQ=-69 GT:PL:GQ 1/1:212,42,0:81
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
614 19 8348441 . T A 62.3 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,2,3;MQ=25;FQ=-42 GT:PL:GQ 1/1:95,15,0:27
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
615 19 8348471 . C T 222 . DP=32;AF1=1;CI95=1,1;DP4=0,0,16,16;MQ=33;FQ=-123 GT:PL:GQ 1/1:255,96,0:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
616 19 8348485 . G A 102 . DP=40;AF1=1;CI95=1,1;DP4=0,0,21,18;MQ=34;FQ=-144 GT:PL:GQ 1/1:135,117,0:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
617 19 8348498 . G A 217 . DP=52;AF1=1;CI95=1,1;DP4=0,0,29,22;MQ=35;FQ=-181 GT:PL:GQ 1/1:250,154,0:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
618 19 8348514 . T C 212 . DP=59;AF1=1;CI95=1,1;DP4=0,0,35,24;MQ=35;FQ=-205 GT:PL:GQ 1/1:245,178,0:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
619 19 8348590 . A G 172 . DP=20;AF1=1;CI95=1,1;DP4=0,0,14,5;MQ=36;FQ=-84 GT:PL:GQ 1/1:205,57,0:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
620 19 8348635 . T C 146 . DP=12;AF1=1;CI95=1,1;DP4=0,0,2,9;MQ=37;FQ=-60 GT:PL:GQ 1/1:179,33,0:63
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
621 19 8348642 . T C 222 . DP=16;AF1=1;CI95=1,1;DP4=0,0,3,13;MQ=37;FQ=-75 GT:PL:GQ 1/1:255,48,0:93
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
622 19 8348695 . T TA 214 . INDEL;DP=18;AF1=1;CI95=1,1;DP4=0,0,4,13;MQ=37;FQ=-85.5 GT:PL:GQ 1/1:255,51,0:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
623 19 8348701 . C T 155 . DP=18;AF1=1;CI95=1,1;DP4=0,0,4,14;MQ=37;FQ=-81 GT:PL:GQ 1/1:188,54,0:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
624 19 8348922 . T C 222 . DP=13;AF1=1;CI95=1,1;DP4=0,0,7,5;MQ=37;FQ=-63 GT:PL:GQ 1/1:255,36,0:69
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
625 19 8348969 . T C 161 . DP=15;AF1=1;CI95=1,1;DP4=0,0,8,7;MQ=37;FQ=-72 GT:PL:GQ 1/1:194,45,0:87
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
626 19 8349035 . G A 50.1 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,5,1;MQ=33;FQ=-45 GT:PL:GQ 1/1:83,18,0:33
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
627 19 8349037 . G A 56.1 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,5,1;MQ=33;FQ=-45 GT:PL:GQ 1/1:89,18,0:33
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
628 19 8349080 . A G 33.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=33;FQ=-42 GT:PL:GQ 1/1:66,15,0:27
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
629 19 8349101 . C G 83.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=33;FQ=-42 GT:PL:GQ 1/1:116,15,0:27
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
630 19 8549054 . T G 3.54 . DP=2;AF1=0.5;CI95=0.5,0.5;DP4=0,1,1,0;MQ=37;FQ=3.54;PV4=1,1,1,1 GT:PL:GQ 0/1:31,0,31:29
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
631 19 8553877 . G C 3.54 . DP=2;AF1=0.5;CI95=0.5,0.5;DP4=1,0,0,1;MQ=37;FQ=3.54;PV4=1,1,1,1 GT:PL:GQ 0/1:31,0,31:29
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
632 19 8555072 . A C 4.13 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 0/1:32,3,0:3
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
633 19 8741092 . G T 5.46 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:34,3,0:3
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
634 19 8783635 . C CA 147 . INDEL;DP=23;AF1=0.5;CI95=0.5,0.5;DP4=2,6,10,2;MQ=36;FQ=126;PV4=0.019,1,0.12,0.01 GT:PL:GQ 0/1:185,0,161:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
635 19 8783903 . G GTC 21.3 . INDEL;DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=37;FQ=-40.5 GT:PL:GQ 1/1:60,6,0:10
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
636 19 8812489 . GT G 34.5 . INDEL;DP=5;AF1=0.5;CI95=0.5,0.5;DP4=0,2,2,1;MQ=35;FQ=18.5;PV4=0.4,0.047,0.25,0.0021 GT:PL:GQ 0/1:72,0,53:56
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
637 19 8817010 . C T 3.01 . DP=2;AF1=0.5;CI95=0.5,0.5;DP4=0,1,1,0;MQ=37;FQ=3.01;PV4=1,1,1,1 GT:PL:GQ 0/1:30,0,30:28
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
638 19 8838292 . G A 23 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=37;FQ=-36 GT:PL:GQ 1/1:55,9,0:15
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
639 19 8838395 . C A 3.55 . DP=2;AF1=0.5014;CI95=0.5,0.5;DP4=1,0,0,1;MQ=37;FQ=-6.58;PV4=1,1,1,1 GT:PL:GQ 0/1:31,0,22:26
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
640 19 8841856 . G GCA 36.5 . INDEL;DP=8;AF1=0.5;CI95=0.5,0.5;DP4=2,1,0,4;MQ=36;FQ=38.3;PV4=0.14,0.19,0.22,0.058 GT:PL:GQ 0/1:74,0,79:76
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
641 19 8850152 . G C 5.46 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:34,3,0:3
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
642 19 8895305 . T A 7.8 . DP=20;AF1=0.5;CI95=0.5,0.5;DP4=3,5,3,1;MQ=37;FQ=10.4;PV4=0.55,0.0027,1,1.9e-09 GT:PL:GQ 0/1:37,0,157:39
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
643 19 8899002 . T G 16.1 . DP=39;AF1=0.5;CI95=0.5,0.5;DP4=2,3,7,0;MQ=36;FQ=19.1;PV4=0.045,0.00068,1,1 GT:PL:GQ 0/1:46,0,85:49
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
644 19 8900459 . C G 7.8 . DP=6;AF1=0.5;CI95=0.5,0.5;DP4=1,1,0,3;MQ=37;FQ=10.4;PV4=0.4,0.0097,1,0.0075 GT:PL:GQ 0/1:37,0,59:39
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
645 19 8900460 . AG AGG 24.5 . INDEL;DP=6;AF1=0.5;CI95=0.5,0.5;DP4=1,1,1,1;MQ=37;FQ=21.3;PV4=1,1,1,0.012 GT:PL:GQ 0/1:62,0,57:59
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
646 19 8900589 . AGG AG 16.6 . INDEL;DP=5;AF1=0.5;CI95=0.5,0.5;DP4=0,2,0,2;MQ=37;FQ=17.4;PV4=1,0.31,1,0.03 GT:PL:GQ 0/1:54,0,56:55
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
647 19 8901128 . T TG 15.6 . INDEL;DP=6;AF1=0.5;CI95=0.5,0.5;DP4=0,2,0,3;MQ=37;FQ=6.39;PV4=1,0.37,1,0.00012 GT:PL:GQ 0/1:53,0,40:43
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
648 19 8904439 . TGG TG 75.5 . INDEL;DP=15;AF1=0.5;CI95=0.5,0.5;DP4=2,1,3,3;MQ=35;FQ=43.5;PV4=1,0.004,0.16,0.034 GT:PL:GQ 0/1:113,0,78:81
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
649 19 8904440 . G GT 66.5 . INDEL;DP=13;AF1=0.5;CI95=0.5,0.5;DP4=2,1,4,2;MQ=35;FQ=43.5;PV4=1,0.044,0.16,0.036 GT:PL:GQ 0/1:104,0,78:81
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
650 19 8905828 . T A 4.77 . DP=7;AF1=0.4999;CI95=0.5,0.5;DP4=2,0,3,0;MQ=37;FQ=6.95;PV4=1,0.007,1,0.11 GT:PL:GQ 0/1:33,0,53:33
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
651 19 8920813 . CGG CG 10.8 . INDEL;DP=6;AF1=0.5;CI95=0.5,0.5;DP4=0,2,0,2;MQ=37;FQ=13.1;PV4=1,0.0022,1,0.012 GT:PL:GQ 0/1:48,0,56:50
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
652 19 8927995 . C T 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
653 19 8948001 . C G 23 . DP=9;AF1=0.5;CI95=0.5,0.5;DP4=0,2,1,2;MQ=37;FQ=22.5;PV4=1,0.0043,1,0.27 GT:PL:GQ 0/1:53,0,52:52
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
654 19 8966507 . A G 5.46 . DP=6;AF1=0.4999;CI95=0.5,0.5;DP4=1,3,2,0;MQ=37;FQ=7.8;PV4=0.4,0.16,1,0.22 GT:PL:GQ 0/1:34,0,99:34
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
655 19 8977007 . GA G 22.2 . INDEL;DP=5;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-40.5 GT:PL:GQ 1/1:61,6,0:10
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
656 19 8977011 . G A 79.1 . DP=10;AF1=1;CI95=1,1;DP4=0,0,2,5;MQ=37;FQ=-48 GT:PL:GQ 1/1:112,21,0:39
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
657 19 8979553 . G GC 41.5 . INDEL;DP=4;AF1=0.501;CI95=0.5,0.5;DP4=0,1,3,0;MQ=37;FQ=-10.9;PV4=0.25,1,1,1 GT:PL:GQ 0/1:79,0,24:27
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
658 19 8981699 . C CA 22.2 . INDEL;DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=37;FQ=-40.5 GT:PL:GQ 1/1:61,6,0:10
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
659 19 8989644 . A C 3.41 . DP=11;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=37;FQ=-33 GT:PL:GQ 1/1:32,6,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
660 19 8989891 . C T 8.65 . DP=5;AF1=0.5005;CI95=0.5,0.5;DP4=0,1,1,1;MQ=37;FQ=-3.17;PV4=1,0.18,1,0.16 GT:PL:GQ 0/1:38,0,27:31
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
661 19 8990112 . C A 7.59 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-33 GT:PL:GQ 1/1:38,6,0:7
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
662 19 8999131 . A G 3.55 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 0/1:31,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
663 19 9010575 . T G 3.56 . DP=2;AF1=0.503;CI95=0.5,0.5;DP4=1,0,1,0;MQ=32;FQ=-8.86;PV4=1,1,1,1 GT:PL:GQ 0/1:31,0,19:25
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
664 19 9010791 . C A 7.8 . DP=6;AF1=0.5;CI95=0.5,0.5;DP4=1,2,0,3;MQ=37;FQ=10.4;PV4=1,0.0042,1,0.093 GT:PL:GQ 0/1:37,0,84:39
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
665 19 9020243 . TA T 18.5 . INDEL;DP=8;AF1=0.5;CI95=0.5,0.5;DP4=0,4,1,2;MQ=36;FQ=21.5;PV4=0.43,0.00079,0.14,0.18 GT:PL:GQ 0/1:56,0,93:59
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
666 19 9066341 . G T 3.01 . DP=2;AF1=0.4999;CI95=0.5,0.5;DP4=0,1,0,1;MQ=37;FQ=3.25;PV4=1,1,1,1 GT:PL:GQ 0/1:30,0,31:28
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
667 19 9096827 . A G 6.98 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:36,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
668 19 9097851 . C A 3.54 . DP=2;AF1=0.5;CI95=0.5,0.5;DP4=0,1,0,1;MQ=37;FQ=3.54;PV4=1,1,1,1 GT:PL:GQ 0/1:31,0,31:29
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
669 19 9100285 . G T 3.59 . DP=2;AF1=0.51;CI95=0.5,0.5;DP4=1,0,1,0;MQ=37;FQ=-13.3;PV4=1,1,1,1 GT:PL:GQ 0/1:31,0,14:21
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
670 19 9126825 . A T 6.98 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:36,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
671 19 9148172 . T C 4.77 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 0/1:33,3,0:3
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
672 19 9216844 . T A 4.13 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 0/1:32,3,0:3
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
673 19 9358012 . G A 164 . DP=11;AF1=1;CI95=1,1;DP4=0,0,10,1;MQ=37;FQ=-60 GT:PL:GQ 1/1:197,33,0:63
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
674 19 9358045 . C A 191 . DP=22;AF1=1;CI95=1,1;DP4=0,0,15,6;MQ=37;FQ=-90 GT:PL:GQ 1/1:224,63,0:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
675 19 9358292 . A G 167 . DP=58;AF1=1;CI95=1,1;DP4=0,0,27,24;MQ=37;FQ=-181 GT:PL:GQ 1/1:200,154,0:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
676 19 9358454 . G A 222 . DP=78;AF1=1;CI95=1,1;DP4=0,0,42,36;MQ=37;FQ=-262 GT:PL:GQ 1/1:255,235,0:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
677 19 9358486 . T G 158 . DP=62;AF1=1;CI95=1,1;DP4=0,0,25,32;MQ=37;FQ=-199 GT:PL:GQ 1/1:191,172,0:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
678 19 9358567 . A G 222 . DP=50;AF1=1;CI95=1,1;DP4=0,0,11,39;MQ=37;FQ=-178 GT:PL:GQ 1/1:255,151,0:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
679 19 9632540 . A G 222 . DP=19;AF1=1;CI95=1,1;DP4=0,0,11,7;MQ=37;FQ=-81 GT:PL:GQ 1/1:255,54,0:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
680 19 9632576 . A G 222 . DP=27;AF1=1;CI95=1,1;DP4=0,0,16,10;MQ=37;FQ=-105 GT:PL:GQ 1/1:255,78,0:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
681 19 9632798 . A G 140 . DP=29;AF1=1;CI95=1,1;DP4=0,0,14,14;MQ=37;FQ=-111 GT:PL:GQ 1/1:173,84,0:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
682 19 9633610 . T C 30.8 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=32;FQ=-33 GT:PL:GQ 1/1:62,6,0:10
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
683 19 9633663 . T G 40 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,1;MQ=30;FQ=-36 GT:PL:GQ 1/1:72,9,0:16
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
684 19 9633666 . A G 39 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,1;MQ=30;FQ=-36 GT:PL:GQ 1/1:71,9,0:16
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
685 19 9681721 . G A 148 . DP=11;AF1=0.5;CI95=0.5,0.5;DP4=3,0,5,3;MQ=35;FQ=36;PV4=0.49,0.19,0.19,1 GT:PL:GQ 0/1:178,0,63:66
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
686 19 9681741 . A T 81 . DP=8;AF1=1;CI95=1,1;DP4=0,0,6,2;MQ=34;FQ=-51 GT:PL:GQ 1/1:114,24,0:45
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
687 19 9681750 . T A 61.1 . DP=7;AF1=1;CI95=1,1;DP4=0,0,6,1;MQ=34;FQ=-48 GT:PL:GQ 1/1:94,21,0:39
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
688 19 9681756 . G A 45.3 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=33;FQ=-42 GT:PL:GQ 1/1:78,15,0:27
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
689 19 9681764 . A T 39.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=32;FQ=-39 GT:PL:GQ 1/1:72,12,0:21
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
690 19 9684345 . A G 6.98 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:36,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
691 19 9952338 . C T 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
692 19 10057473 . G GTC 75.5 . INDEL;DP=29;AF1=0.5;CI95=0.5,0.5;DP4=1,4,10,0;MQ=33;FQ=73;PV4=0.0037,0.17,0.012,1 GT:PL:GQ 0/1:113,0,109:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
693 19 10059270 . G C 21 . DP=35;AF1=0.5;CI95=0.5,0.5;DP4=4,11,0,9;MQ=36;FQ=24;PV4=0.26,3e-14,0.0078,3.5e-05 GT:PL:GQ 0/1:51,0,255:54
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
694 19 10060151 . CAAA CAA 27.2 . INDEL;DP=2;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-40.5 GT:PL:GQ 1/1:66,6,0:10
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
695 19 10126690 . A AC 14.6 . INDEL;DP=4;AF1=0.5;CI95=0.5,0.5;DP4=0,2,2,0;MQ=37;FQ=16.1;PV4=0.33,1,1,0.0011 GT:PL:GQ 0/1:52,0,56:53
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
696 19 10130185 . GT G 33.4 . INDEL;DP=5;AF1=1;CI95=0.5,1;DP4=0,0,2,1;MQ=30;FQ=-43.5 GT:PL:GQ 1/1:73,9,0:16
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
697 19 10133086 . A G 170 . DP=27;AF1=0.5;CI95=0.5,0.5;DP4=10,6,7,4;MQ=37;FQ=173;PV4=1,0.5,1,1 GT:PL:GQ 0/1:200,0,255:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
698 19 10153682 . A C 4.77 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 0/1:33,3,0:3
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
699 19 10157183 . G T 35 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,1;MQ=37;FQ=-36 GT:PL:GQ 1/1:67,9,0:16
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
700 19 10163595 . A AG 27.2 . INDEL;DP=4;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-40.5 GT:PL:GQ 1/1:66,6,0:10
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
701 19 10250372 . G A 32 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=33;FQ=-36 GT:PL:GQ 1/1:64,9,0:16
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
702 19 10250380 . A G 72.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,1,4;MQ=35;FQ=-42 GT:PL:GQ 1/1:105,15,0:27
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
703 19 10250405 . A G 159 . DP=9;AF1=1;CI95=1,1;DP4=0,0,4,4;MQ=32;FQ=-51 GT:PL:GQ 1/1:192,24,0:45
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
704 19 10250417 . T C 222 . DP=13;AF1=1;CI95=1,1;DP4=0,0,9,4;MQ=33;FQ=-66 GT:PL:GQ 1/1:255,39,0:75
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
705 19 10250483 . A T 110 . DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=32;FQ=-51 GT:PL:GQ 1/1:143,24,0:45
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
706 19 10250497 . C G 55 . DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=32;FQ=-51 GT:PL:GQ 1/1:88,24,0:45
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
707 19 10250501 . C T 74 . DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=32;FQ=-51 GT:PL:GQ 1/1:107,24,0:45
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
708 19 10262515 . A T 3.58 . DP=2;AF1=0.5078;CI95=0.5,0.5;DP4=0,1,1,0;MQ=37;FQ=-12.4;PV4=1,1,1,1 GT:PL:GQ 0/1:31,0,15:21
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
709 19 10268290 . T TTC 56.5 . INDEL;DP=5;AF1=0.5016;CI95=0.5,0.5;DP4=0,1,4,0;MQ=37;FQ=-12.8;PV4=0.2,0.49,1,0.13 GT:PL:GQ 0/1:94,0,22:25
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
710 19 10281024 . G T 7.8 . DP=5;AF1=0.5007;CI95=0.5,0.5;DP4=0,1,3,0;MQ=37;FQ=-4.28;PV4=0.25,0.023,1,0.14 GT:PL:GQ 0/1:37,0,25:29
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
711 19 10297732 . TGG TGGGG 50.4 . INDEL;DP=9;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=37;FQ=-43.5 GT:PL:GQ 1/1:90,9,0:16
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
712 19 10498385 . A T 3.54 . DP=2;AF1=0.5;CI95=0.5,0.5;DP4=0,1,1,0;MQ=37;FQ=3.54;PV4=1,1,1,1 GT:PL:GQ 0/1:31,0,31:29
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
713 19 10502388 . A G 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
714 19 10525511 . A C 13.2 . DP=9;AF1=0.5;CI95=0.5,0.5;DP4=4,1,0,4;MQ=33;FQ=16.1;PV4=0.048,0.019,0.0056,1 GT:PL:GQ 0/1:43,0,107:46
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
715 19 10590412 . G C 4.77 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 0/1:33,3,0:3
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
716 19 10607212 . A G 4.13 . DP=7;AF1=0.4998;CI95=0.5,0.5;DP4=1,2,2,0;MQ=37;FQ=6.2;PV4=0.4,0.00041,1,1 GT:PL:GQ 0/1:32,0,89:31
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
717 19 10656785 . TA TAAA 37.4 . INDEL;DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=37;FQ=-43.5 GT:PL:GQ 1/1:77,9,0:16
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
718 19 10663128 . A G 121 . DP=22;AF1=0.5;CI95=0.5,0.5;DP4=5,5,7,5;MQ=37;FQ=124;PV4=1,0.0086,1,1 GT:PL:GQ 0/1:151,0,173:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
719 19 10669900 . TC TCC 21.5 . INDEL;DP=3;AF1=0.5013;CI95=0.5,0.5;DP4=0,1,2,0;MQ=37;FQ=-11.8;PV4=0.33,1,1,0.027 GT:PL:GQ 0/1:59,0,23:26
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
720 19 10681183 . G C 3.54 . DP=2;AF1=0.5;CI95=0.5,0.5;DP4=0,1,0,1;MQ=37;FQ=3.54;PV4=1,1,1,1 GT:PL:GQ 0/1:31,0,31:29
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
721 19 10689339 . TA TAAA 82.7 . INDEL;DP=7;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=37;FQ=-49.5 GT:PL:GQ 1/1:123,15,0:27
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
722 19 10690081 . GT GTTT 23.2 . INDEL;DP=6;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=37;FQ=-40.5 GT:PL:GQ 1/1:62,6,0:10
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
723 19 10698013 . G C 4.61 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-33 GT:PL:GQ 1/1:34,6,0:5
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
724 19 10699336 . AGG AG 73.5 . INDEL;DP=7;AF1=0.5016;CI95=0.5,0.5;DP4=1,0,2,2;MQ=37;FQ=-12.8;PV4=1,1,1,0.14 GT:PL:GQ 0/1:111,0,22:25
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
725 19 10700484 . A C 122 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,4,2;MQ=37;FQ=-45 GT:PL:GQ 1/1:155,18,0:33
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
726 19 10700486 . G GC 95 . INDEL;DP=6;AF1=1;CI95=0.5,1;DP4=0,0,2,2;MQ=37;FQ=-46.5 GT:PL:GQ 1/1:135,12,0:21
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
727 19 10701724 . AGG AG 19.5 . INDEL;DP=12;AF1=0.5;CI95=0.5,0.5;DP4=1,4,2,1;MQ=37;FQ=22.5;PV4=0.46,0.32,1,0.0032 GT:PL:GQ 0/1:57,0,130:60
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
728 19 10702354 . T TCTGG 73 . INDEL;DP=10;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=37;FQ=-46.5 GT:PL:GQ 1/1:113,12,0:21
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
729 19 10773851 . G T 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
730 19 10788446 . T C 13.2 . DP=32;AF1=0.5;CI95=0.5,0.5;DP4=12,1,0,7;MQ=37;FQ=16.1;PV4=0.0001,0.00062,1,1 GT:PL:GQ 0/1:43,0,165:46
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
731 19 10924486 . T C 3.55 . DP=2;AF1=0.5006;CI95=0.5,0.5;DP4=0,1,0,1;MQ=37;FQ=-4.74;PV4=1,1,1,1 GT:PL:GQ 0/1:31,0,25:28
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
732 19 10927766 . G GAT 11.8 . INDEL;DP=5;AF1=0.5;CI95=0.5,0.5;DP4=0,3,1,1;MQ=37;FQ=14.6;PV4=0.4,0.22,1,0.0014 GT:PL:GQ 0/1:49,0,79:51
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
733 19 10947182 . G C 41.8 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-33 GT:PL:GQ 1/1:73,6,0:10
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
734 19 10948976 . TC TCC 64.9 . INDEL;DP=7;AF1=0.5554;CI95=0.5,1;DP4=1,0,3,2;MQ=35;FQ=-27.5;PV4=1,0.27,1,0.35 GT:PL:GQ 0/1:102,0,7:10
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
735 19 10972143 . G T 8.44 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-33 GT:PL:GQ 1/1:39,6,0:8
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
736 19 10975413 . C CA 12.5 . INDEL;DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=37;FQ=-40.5 GT:PL:GQ 1/1:51,6,0:9
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
737 19 11017779 . TC TCAC 16.3 . INDEL;DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=32;FQ=-40.5 GT:PL:GQ 1/1:55,6,0:10
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
738 19 11122585 . T TC 53.7 . INDEL;DP=9;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=33;FQ=-49.5 GT:PL:GQ 1/1:94,15,0:27
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
739 19 11165572 . A G 222 . DP=16;AF1=1;CI95=1,1;DP4=0,0,10,6;MQ=37;FQ=-75 GT:PL:GQ 1/1:255,48,0:93
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
740 19 11165677 . G A 49.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,3,3;MQ=37;FQ=-45 GT:PL:GQ 1/1:82,18,0:33
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
741 19 11165689 . T A 85.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,3,3;MQ=37;FQ=-45 GT:PL:GQ 1/1:118,18,0:33
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
742 19 11165712 . A G 57.3 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,3,2;MQ=37;FQ=-42 GT:PL:GQ 1/1:90,15,0:27
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
743 19 11196378 . CTTT CTTTT 214 . INDEL;DP=34;AF1=1;CI95=1,1;DP4=0,0,18,15;MQ=37;FQ=-134 GT:PL:GQ 1/1:255,99,0:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
744 19 11196544 . C T 141 . DP=19;AF1=1;CI95=1,1;DP4=0,0,7,11;MQ=37;FQ=-81 GT:PL:GQ 1/1:174,54,0:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
745 19 11196769 . A G 174 . DP=23;AF1=1;CI95=1,1;DP4=0,0,6,15;MQ=37;FQ=-90 GT:PL:GQ 1/1:207,63,0:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
746 19 11402540 . TC T 32.4 . INDEL;DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=37;FQ=-43.5 GT:PL:GQ 1/1:72,9,0:16
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
747 19 11465876 . C T 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
748 19 11467556 . ATGTGTGTGTGTGTGT ATGTGTGTGTGTGT 216 . INDEL;DP=92;AF1=0.5;CI95=0.5,0.5;DP4=19,27,6,22;MQ=37;FQ=217;PV4=0.13,0.00092,0.36,1 GT:PL:GQ 0/1:254,0,255:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
749 19 11472871 . G T 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
750 19 11489280 . A T 13 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=32;FQ=-33 GT:PL:GQ 1/1:44,6,0:9
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
751 19 11537444 . C CG 48.5 . INDEL;DP=6;AF1=0.5016;CI95=0.5,0.5;DP4=1,0,0,4;MQ=37;FQ=-12.8;PV4=0.2,0.18,1,1 GT:PL:GQ 0/1:86,0,22:25
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
752 19 11544046 . G GCT 74.5 . INDEL;DP=28;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=35;FQ=-61.5 GT:PL:GQ 1/1:115,27,0:51
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
753 19 11546250 . A G 3.54 . DP=2;AF1=0.5;CI95=0.5,0.5;DP4=0,1,1,0;MQ=37;FQ=3.54;PV4=1,1,1,1 GT:PL:GQ 0/1:31,0,31:29
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
754 19 11583902 . A C 3.54 . DP=2;AF1=0.5001;CI95=0.5,0.5;DP4=1,0,0,1;MQ=37;FQ=-3.07;PV4=1,1,1,1 GT:PL:GQ 0/1:31,0,29:29
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
755 19 11593164 . G GCC 121 . INDEL;DP=16;AF1=1;CI95=0.5,1;DP4=1,0,15,0;MQ=36;FQ=-45.5;PV4=1,1,0.36,0.34 GT:PL:GQ 1/1:161,11,0:19
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
756 19 11593167 . A G 32 . DP=16;AF1=1;CI95=0.5,1;DP4=1,0,10,0;MQ=37;FQ=-30;PV4=1,0.0089,1,1 GT:PL:GQ 1/1:62,3,0:6
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
757 19 11632363 . A AGT 45.4 . INDEL;DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=37;FQ=-43.5 GT:PL:GQ 1/1:85,9,0:16
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
758 19 11660704 . GAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAG GAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAG 8.83 . INDEL;DP=6;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=37;FQ=-40.5 GT:PL:GQ 1/1:47,6,0:8
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
759 19 11661671 . TC TCC 29.2 . INDEL;DP=3;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-40.5 GT:PL:GQ 1/1:68,6,0:10
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
760 19 11676455 . CT C 14.6 . INDEL;DP=9;AF1=0.5;CI95=0.5,0.5;DP4=0,2,1,1;MQ=37;FQ=14.1;PV4=1,0.25,1,0.23 GT:PL:GQ 0/1:52,0,51:51
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
761 19 11677634 . A G 15.1 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=30;FQ=-36 GT:PL:GQ 1/1:47,9,0:14
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
762 19 11777860 . A G 49.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,2;MQ=25;FQ=-39 GT:PL:GQ 1/1:82,12,0:21
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
763 19 11777864 . C G 51.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,2;MQ=25;FQ=-39 GT:PL:GQ 1/1:84,12,0:21
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
764 19 11777878 . C G 58.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,2;MQ=25;FQ=-39 GT:PL:GQ 1/1:91,12,0:21
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
765 19 11777923 . T C 47.5 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,3,1;MQ=28;FQ=-39 GT:PL:GQ 1/1:80,12,0:21
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
766 19 11777948 . C G 43.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,1;MQ=28;FQ=-39 GT:PL:GQ 1/1:76,12,0:21
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
767 19 11839957 . A G 38.1 . DP=10;AF1=0.5064;CI95=0.5,0.5;DP4=0,1,4,2;MQ=34;FQ=-11.3;PV4=0.43,0.0041,0.29,0.17 GT:PL:GQ 0/1:68,0,16:19
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
768 19 11839959 . A G 32.1 . DP=11;AF1=0.508;CI95=0.5,0.5;DP4=0,1,4,2;MQ=34;FQ=-12.3;PV4=0.43,0.0011,0.29,0.17 GT:PL:GQ 0/1:62,0,15:18
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
769 19 11839992 . A G 106 . DP=18;AF1=1;CI95=0.5,1;DP4=0,1,13,3;MQ=35;FQ=-41;PV4=0.24,3.8e-07,0.33,0.34 GT:PL:GQ 1/1:139,14,0:25
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
770 19 11840001 . T C 112 . DP=20;AF1=1;CI95=1,1;DP4=0,1,15,3;MQ=35;FQ=-47;PV4=0.21,7.2e-06,0.34,0.37 GT:PL:GQ 1/1:145,20,0:37
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
771 19 11840069 . T C 86.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,5,1;MQ=37;FQ=-45 GT:PL:GQ 1/1:119,18,0:33
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
772 19 11840074 . GATCATCA GATCA 60.4 . INDEL;DP=5;AF1=1;CI95=0.5,1;DP4=0,0,2,1;MQ=37;FQ=-43.5 GT:PL:GQ 1/1:100,9,0:16
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
773 19 11840087 . A G 19.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-33 GT:PL:GQ 1/1:51,6,0:10
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
774 19 11840209 . A G 76.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,2,3;MQ=25;FQ=-42 GT:PL:GQ 1/1:109,15,0:27
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
775 19 11840219 . C G 66.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,2,3;MQ=25;FQ=-42 GT:PL:GQ 1/1:99,15,0:27
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
776 19 11840229 . T G 65.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,2,3;MQ=25;FQ=-42 GT:PL:GQ 1/1:98,15,0:27
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
777 19 11840237 . A T 42.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,2,3;MQ=25;FQ=-42 GT:PL:GQ 1/1:75,15,0:27
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
778 19 11840260 . G C 35.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,2;MQ=25;FQ=-39 GT:PL:GQ 1/1:68,12,0:21
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
779 19 11904739 . A G 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
780 19 11952270 . A G 222 . DP=34;AF1=1;CI95=1,1;DP4=0,1,13,20;MQ=35;FQ=-92;PV4=1,0.16,0.29,1 GT:PL:GQ 1/1:255,65,0:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
781 19 11952283 . T C 165 . DP=38;AF1=1;CI95=1,1;DP4=0,0,14,21;MQ=35;FQ=-132 GT:PL:GQ 1/1:198,105,0:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
782 19 11952293 . A G 222 . DP=45;AF1=1;CI95=1,1;DP4=0,0,19,25;MQ=34;FQ=-159 GT:PL:GQ 1/1:255,132,0:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
783 19 11952355 . G C 21.3 . DP=14;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=30;FQ=-42 GT:PL:GQ 1/1:54,15,0:26
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
784 19 11952357 . T C 39.1 . DP=14;AF1=1;CI95=0.5,1;DP4=0,0,5,1;MQ=32;FQ=-45 GT:PL:GQ 1/1:72,18,0:33
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
785 19 11952381 . C T 82.1 . DP=8;AF1=1;CI95=1,1;DP4=0,0,5,2;MQ=36;FQ=-48 GT:PL:GQ 1/1:115,21,0:39
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
786 19 11952422 . CTC CTCGTC 88.7 . INDEL;DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=37;FQ=-49.5 GT:PL:GQ 1/1:129,15,0:27
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
787 19 11952453 . T C 88.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=37;FQ=-42 GT:PL:GQ 1/1:121,15,0:27
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
788 19 11952566 . C G 112 . DP=9;AF1=1;CI95=1,1;DP4=0,0,5,4;MQ=37;FQ=-54 GT:PL:GQ 1/1:145,27,0:51
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
789 19 11952602 . C T 186 . DP=21;AF1=1;CI95=1,1;DP4=0,0,12,9;MQ=37;FQ=-90 GT:PL:GQ 1/1:219,63,0:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
790 19 11952628 . CTCTTCT CTCT 15.6 . INDEL;DP=28;AF1=0.5;CI95=0.5,0.5;DP4=10,13,3,1;MQ=37;FQ=18.5;PV4=0.33,1,1,1 GT:PL:GQ 0/1:53,0,255:56
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
791 19 11952659 . A C 172 . DP=21;AF1=1;CI95=1,1;DP4=0,0,9,12;MQ=37;FQ=-90 GT:PL:GQ 1/1:205,63,0:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
792 19 11952675 . T C 178 . DP=17;AF1=1;CI95=1,1;DP4=0,0,8,8;MQ=37;FQ=-75 GT:PL:GQ 1/1:211,48,0:93
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
793 19 11952711 . TA T 31.5 . INDEL;DP=11;AF1=0.5;CI95=0.5,0.5;DP4=0,4,1,2;MQ=37;FQ=34.4;PV4=0.43,1,1,0.0096 GT:PL:GQ 0/1:69,0,86:72
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
794 19 11952712 . AGCTGCTGCTGCTGC AGCTGCTGCTGCTGCTGC 99.6 . INDEL;DP=9;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=37;FQ=-52.5 GT:PL:GQ 1/1:140,18,0:33
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
795 19 11952805 . A G 198 . DP=21;AF1=1;CI95=1,1;DP4=0,0,8,12;MQ=37;FQ=-87 GT:PL:GQ 1/1:231,60,0:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
796 19 11952841 . T G 191 . DP=24;AF1=1;CI95=1,1;DP4=0,0,16,7;MQ=36;FQ=-96 GT:PL:GQ 1/1:224,69,0:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
797 19 11952882 . A C 140 . DP=28;AF1=1;CI95=1,1;DP4=0,0,22,6;MQ=34;FQ=-111 GT:PL:GQ 1/1:173,84,0:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
798 19 11952895 . A G 104 . DP=25;AF1=1;CI95=1,1;DP4=0,0,21,1;MQ=34;FQ=-93 GT:PL:GQ 1/1:137,66,0:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
799 19 11997967 . G C 6.98 . DP=3;AF1=0.5003;CI95=0.5,0.5;DP4=1,0,2,0;MQ=33;FQ=3.2;PV4=1,0.019,0.33,1 GT:PL:GQ 0/1:36,0,28:31
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
800 19 12033202 . G A 27 . DP=4;AF1=0.5008;CI95=0.5,0.5;DP4=0,1,1,2;MQ=28;FQ=-4.12;PV4=1,0.048,0,0.22 GT:PL:GQ 0/1:57,0,25:28
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
801 19 12033225 . T G 178 . DP=15;AF1=1;CI95=0.5,1;DP4=0,1,5,7;MQ=34;FQ=-29;PV4=1,0.23,0.26,0.1 GT:PL:GQ 1/1:207,2,0:5
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
802 19 12033238 . T C 222 . DP=23;AF1=1;CI95=1,1;DP4=0,1,10,9;MQ=35;FQ=-50;PV4=1,0.39,0.32,0.24 GT:PL:GQ 1/1:255,23,0:43
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
803 19 12033263 . A G 222 . DP=32;AF1=1;CI95=1,1;DP4=0,0,15,15;MQ=36;FQ=-117 GT:PL:GQ 1/1:255,90,0:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
804 19 12033304 . A G 222 . DP=41;AF1=1;CI95=1,1;DP4=0,0,18,23;MQ=36;FQ=-150 GT:PL:GQ 1/1:255,123,0:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
805 19 12033367 . A C 152 . DP=32;AF1=1;CI95=1,1;DP4=0,0,11,19;MQ=37;FQ=-117 GT:PL:GQ 1/1:185,90,0:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
806 19 12033372 . TC TCC 214 . INDEL;DP=30;AF1=1;CI95=1,1;DP4=0,0,11,18;MQ=37;FQ=-122 GT:PL:GQ 1/1:255,87,0:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
807 19 12033396 . T C 192 . DP=21;AF1=1;CI95=1,1;DP4=0,0,9,11;MQ=37;FQ=-87 GT:PL:GQ 1/1:225,60,0:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
808 19 12033437 . A G 181 . DP=8;AF1=1;CI95=1,1;DP4=0,0,4,4;MQ=37;FQ=-51 GT:PL:GQ 1/1:214,24,0:45
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
809 19 12052486 . T C 3.55 . DP=2;AF1=0.5011;CI95=0.5,0.5;DP4=1,0,0,1;MQ=37;FQ=-5.91;PV4=1,1,1,1 GT:PL:GQ 0/1:31,0,23:27
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
810 19 12063068 . G C 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
811 19 12075788 . A T 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
812 19 12596319 . G C 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
813 19 12761248 . C T 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
814 19 12761275 . G A 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
815 19 12845038 . AT ATT 11.5 . INDEL;DP=2;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-40.5 GT:PL:GQ 1/1:50,6,0:9
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
816 19 12873388 . C T 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
817 19 12979639 . A T 4.77 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 0/1:33,3,0:3
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
818 19 12979730 . T C 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
819 19 12979796 . G A 25.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=32;FQ=-33 GT:PL:GQ 1/1:57,6,0:10
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
820 19 12980273 . G A 29 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,1,2;MQ=37;FQ=-36 GT:PL:GQ 1/1:61,9,0:16
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
821 19 12980707 . A G 86 . DP=10;AF1=1;CI95=1,1;DP4=0,0,3,6;MQ=37;FQ=-54 GT:PL:GQ 1/1:119,27,0:51
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
822 19 12980733 . G A 124 . DP=13;AF1=1;CI95=1,1;DP4=0,0,4,9;MQ=37;FQ=-66 GT:PL:GQ 1/1:157,39,0:75
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
823 19 12980760 . C G 222 . DP=15;AF1=1;CI95=1,1;DP4=0,0,3,12;MQ=37;FQ=-72 GT:PL:GQ 1/1:255,45,0:87
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
824 19 12980967 . G A 104 . DP=10;AF1=1;CI95=1,1;DP4=0,0,3,6;MQ=37;FQ=-54 GT:PL:GQ 1/1:137,27,0:51
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
825 19 12981016 . T C 222 . DP=15;AF1=1;CI95=1,1;DP4=0,0,9,6;MQ=37;FQ=-72 GT:PL:GQ 1/1:255,45,0:87
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
826 19 13670070 . C T 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=25;FQ=-33 GT:PL:GQ 1/1:45,6,0:10
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
827 19 13670140 . C T 28 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=25;FQ=-36 GT:PL:GQ 1/1:60,9,0:16
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
828 19 13670153 . A G 30 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=25;FQ=-36 GT:PL:GQ 1/1:62,9,0:16
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
829 19 13670161 . G A 27 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=25;FQ=-36 GT:PL:GQ 1/1:59,9,0:16
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
830 19 14007582 . C A 3.98 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=37;FQ=-33 GT:PL:GQ 1/1:33,6,0:5
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
831 19 14007612 . AAGAGAG AAGAG 28.2 . INDEL;DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=37;FQ=-40.5 GT:PL:GQ 1/1:67,6,0:10
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
832 19 14070075 . T A 3.55 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 0/1:31,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
833 19 14524333 . TAG T 14.6 . INDEL;DP=4;AF1=0.5004;CI95=0.5,0.5;DP4=1,0,1,1;MQ=37;FQ=-7.41;PV4=1,1,1,0.39 GT:PL:GQ 0/1:52,0,28:31
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
834 19 14527043 . T A 3.54 . DP=2;AF1=0.5;CI95=0.5,0.5;DP4=1,0,0,1;MQ=37;FQ=3.54;PV4=1,1,1,1 GT:PL:GQ 0/1:31,0,31:29
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
835 19 14580308 . T A 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
836 19 14592466 . GC GCCC 22.2 . INDEL;DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=37;FQ=-40.5 GT:PL:GQ 1/1:61,6,0:10
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
837 19 14607703 . T C 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
838 19 15533970 . T C 51 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,1,2;MQ=30;FQ=-36 GT:PL:GQ 1/1:83,9,0:16
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
839 19 15533994 . A G 45.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,1,3;MQ=32;FQ=-39 GT:PL:GQ 1/1:78,12,0:21
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
840 19 15534018 . A G 42.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,1,3;MQ=32;FQ=-39 GT:PL:GQ 1/1:75,12,0:21
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
841 19 15647552 . C A 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
842 19 16143433 . T G 4.77 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 0/1:33,3,0:3
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
843 19 16143436 . A C 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
844 19 16213914 . G A 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
845 19 16296200 . A G 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
846 19 16298173 . C A 3.54 . DP=2;AF1=0.5;CI95=0.5,0.5;DP4=0,1,0,1;MQ=37;FQ=3.54;PV4=1,1,1,1 GT:PL:GQ 0/1:31,0,31:29
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
847 19 16304596 . G C 3.54 . DP=2;AF1=0.5001;CI95=0.5,0.5;DP4=1,0,0,1;MQ=37;FQ=3.25;PV4=1,1,1,1 GT:PL:GQ 0/1:31,0,30:29
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
848 19 16471631 . T C 3.55 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 0/1:31,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
849 19 16548752 . G T 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
850 19 16631177 . C A 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
851 19 16735479 . G T 6.98 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:36,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
852 19 16737011 . C G 3.55 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 0/1:31,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
853 19 16751327 . G A 3.55 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 0/1:31,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
854 19 16800107 . T C 3.54 . DP=3;AF1=0.5;CI95=0.5,0.5;DP4=1,0,0,1;MQ=37;FQ=3.54;PV4=1,1,1,1 GT:PL:GQ 0/1:31,0,31:29
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
855 19 17419010 . C T 3.54 . DP=2;AF1=0.5;CI95=0.5,0.5;DP4=1,0,1,0;MQ=37;FQ=3.54;PV4=1,1,1,1 GT:PL:GQ 0/1:31,0,31:29
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
856 19 17752449 . T C 4.77 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 0/1:33,3,0:3
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
857 19 17767368 . C T 152 . DP=13;AF1=1;CI95=1,1;DP4=0,0,6,7;MQ=36;FQ=-66 GT:PL:GQ 1/1:185,39,0:75
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
858 19 17767372 . G A 161 . DP=13;AF1=1;CI95=1,1;DP4=0,0,6,7;MQ=36;FQ=-66 GT:PL:GQ 1/1:194,39,0:75
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
859 19 18001132 . G A 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
860 19 18001229 . G C 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=37;FQ=-33 GT:PL:GQ 1/1:45,6,0:10
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
861 19 18001743 . A G 3.02 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 0/1:30,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
862 19 18001767 . T C 6.2 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:35,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
863 19 18195972 . C T 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
864 19 18484588 . A G 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
865 19 18664889 . A ATG 27.5 . INDEL;DP=11;AF1=0.5016;CI95=0.5,0.5;DP4=0,1,0,4;MQ=35;FQ=-12.8;PV4=1,0.18,0.34,0.42 GT:PL:GQ 0/1:65,0,22:25
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
866 19 18671826 . T C 6.2 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:35,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
867 19 18703713 . T G 4.13 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 0/1:32,3,0:3
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
868 19 20260046 . C A 3.55 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 0/1:31,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
869 19 20449580 . A T 4.13 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 0/1:32,3,0:3
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
870 19 20452978 . GCC GCCC 102 . INDEL;DP=13;AF1=0.5;CI95=0.5,0.5;DP4=2,1,1,5;MQ=37;FQ=32.5;PV4=0.23,1,1,2.4e-05 GT:PL:GQ 0/1:140,0,67:70
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
871 19 20454525 . C G 3.55 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 0/1:31,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
872 19 20697944 . G GC 106 . INDEL;DP=13;AF1=0.6243;CI95=0.5,1;DP4=0,1,9,1;MQ=36;FQ=-30.5;PV4=0.18,0.19,0.38,0.11 GT:PL:GQ 0/1:143,0,4:7
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
873 19 20699318 . A T 34.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,1;MQ=34;FQ=-39 GT:PL:GQ 1/1:67,12,0:21
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
874 19 20705340 . G GATT 28.5 . INDEL;DP=5;AF1=0.5008;CI95=0.5,0.5;DP4=1,0,3,0;MQ=34;FQ=-9.98;PV4=1,0.13,0.33,0.0037 GT:PL:GQ 0/1:66,0,25:28
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
875 19 20705889 . A C 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
876 19 20711314 . TGG TGGGG 17.5 . INDEL;DP=10;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=33;FQ=-43.5 GT:PL:GQ 1/1:57,9,0:15
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
877 19 20711316 . G GGT 89.6 . INDEL;DP=8;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=35;FQ=-52.5 GT:PL:GQ 1/1:130,18,0:33
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
878 19 20711320 . G C 32.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=37;FQ=-39 GT:PL:GQ 1/1:65,12,0:21
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
879 19 20715519 . G A 4.77 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 0/1:33,3,0:3
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
880 19 20717383 . G GAACT 25.5 . INDEL;DP=12;AF1=0.5;CI95=0.5,0.5;DP4=1,4,0,3;MQ=36;FQ=28.5;PV4=1,0.48,0.11,0.0065 GT:PL:GQ 0/1:63,0,130:66
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
881 19 21354909 . G A 12.2 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=33;FQ=-36 GT:PL:GQ 1/1:44,9,0:14
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
882 19 21467193 . ACCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTC ACCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTC 63 . INDEL;DP=52;AF1=1;CI95=0.5,1;DP4=0,0,1,3;MQ=37;FQ=-46.5 GT:PL:GQ 1/1:103,12,0:21
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
883 19 21470903 . T C 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
884 19 21470906 . T A 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
885 19 21486985 . T C 28 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,1,2;MQ=37;FQ=-36 GT:PL:GQ 1/1:60,9,0:16
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
886 19 21486986 . A AG 65.4 . INDEL;DP=4;AF1=1;CI95=0.5,1;DP4=0,0,1,2;MQ=37;FQ=-43.5 GT:PL:GQ 1/1:105,9,0:16
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
887 19 21736204 . C G 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
888 19 21744637 . G A 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
889 19 21764018 . T A 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
890 19 21789476 . G T 12 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-33 GT:PL:GQ 1/1:43,6,0:9
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
891 19 21798928 . C A 3.55 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 0/1:31,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
892 19 21897216 . A G 6.2 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:35,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
893 19 21917388 . A G 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
894 19 21919108 . AGG AGGG 14.8 . INDEL;DP=6;AF1=0.5263;CI95=0.5,1;DP4=1,0,1,1;MQ=37;FQ=-24.5;PV4=1,1,1,0 GT:PL:GQ 0/1:52,0,10:13
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
895 19 21936202 . A T 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
896 19 22011899 . A G 96.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,1;MQ=37;FQ=-39 GT:PL:GQ 1/1:129,12,0:21
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
897 19 22011902 . A C 48.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,1;MQ=37;FQ=-39 GT:PL:GQ 1/1:81,12,0:21
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
898 19 22011911 . A T 67.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,4,1;MQ=37;FQ=-42 GT:PL:GQ 1/1:100,15,0:27
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
899 19 22011974 . G A 222 . DP=37;AF1=1;CI95=1,1;DP4=0,0,17,18;MQ=37;FQ=-132 GT:PL:GQ 1/1:255,105,0:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
900 19 22012019 . T C 201 . DP=44;AF1=1;CI95=1,1;DP4=0,0,23,21;MQ=37;FQ=-159 GT:PL:GQ 1/1:234,132,0:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
901 19 22012051 . A G 165 . DP=35;AF1=1;CI95=1,1;DP4=0,0,15,19;MQ=37;FQ=-129 GT:PL:GQ 1/1:198,102,0:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
902 19 22012155 . T A 193 . DP=24;AF1=1;CI95=1,1;DP4=0,0,16,8;MQ=36;FQ=-99 GT:PL:GQ 1/1:226,72,0:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
903 19 22012157 . C G 158 . DP=24;AF1=1;CI95=1,1;DP4=0,0,16,7;MQ=36;FQ=-96 GT:PL:GQ 1/1:191,69,0:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
904 19 22012166 . G C 146 . DP=11;AF1=1;CI95=1,1;DP4=0,0,6,5;MQ=35;FQ=-60 GT:PL:GQ 1/1:179,33,0:63
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
905 19 22012217 . T C 222 . DP=17;AF1=1;CI95=1,1;DP4=0,0,7,8;MQ=36;FQ=-72 GT:PL:GQ 1/1:255,45,0:87
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
906 19 22012250 . A G 179 . DP=25;AF1=1;CI95=1,1;DP4=0,0,8,16;MQ=36;FQ=-99 GT:PL:GQ 1/1:212,72,0:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
907 19 22012307 . T C 222 . DP=22;AF1=1;CI95=1,1;DP4=0,0,6,16;MQ=36;FQ=-93 GT:PL:GQ 1/1:255,66,0:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
908 19 22012325 . A C 217 . DP=12;AF1=1;CI95=1,1;DP4=0,0,4,7;MQ=36;FQ=-60 GT:PL:GQ 1/1:250,33,0:63
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
909 19 22012430 . T C 222 . DP=24;AF1=1;CI95=1,1;DP4=0,0,6,17;MQ=37;FQ=-96 GT:PL:GQ 1/1:255,69,0:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
910 19 22012579 . T A 222 . DP=42;AF1=1;CI95=1,1;DP4=0,0,26,15;MQ=37;FQ=-150 GT:PL:GQ 1/1:255,123,0:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
911 19 22012727 . C T 222 . DP=21;AF1=1;CI95=1,1;DP4=0,0,8,13;MQ=37;FQ=-90 GT:PL:GQ 1/1:255,63,0:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
912 19 22012748 . A G 30.5 . DP=18;AF1=1;CI95=0.5,1;DP4=0,0,3,1;MQ=37;FQ=-39 GT:PL:GQ 1/1:63,12,0:21
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
913 19 22012751 . T C 24 . DP=17;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=37;FQ=-36 GT:PL:GQ 1/1:56,9,0:15
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
914 19 22012760 . C T 222 . DP=16;AF1=1;CI95=1,1;DP4=0,0,5,10;MQ=36;FQ=-72 GT:PL:GQ 1/1:255,45,0:87
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
915 19 22128042 . G A 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
916 19 22376925 . G A 3.55 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 0/1:31,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
917 19 22516053 . A G 54 . DP=9;AF1=1;CI95=1,1;DP4=0,0,3,5;MQ=36;FQ=-51 GT:PL:GQ 1/1:87,24,0:45
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
918 19 23130188 . G A 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
919 19 23216070 . T C 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
920 19 23216752 . T G 6.02 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=32;FQ=-33 GT:PL:GQ 1/1:36,6,0:6
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
921 19 23216754 . G A 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=32;FQ=-33 GT:PL:GQ 1/1:44,6,0:9
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
922 19 23225184 . C T 3.55 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 0/1:31,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
923 19 23239936 . C A 5.46 . DP=19;AF1=0.4999;CI95=0.5,0.5;DP4=5,1,0,6;MQ=35;FQ=7.8;PV4=0.015,0.00042,0.072,1 GT:PL:GQ 0/1:34,0,116:34
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
924 19 23281456 . A G 3.54 . DP=2;AF1=0.5;CI95=0.5,0.5;DP4=1,0,0,1;MQ=37;FQ=3.54;PV4=1,1,1,1 GT:PL:GQ 0/1:31,0,31:29
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
925 19 23309145 . G A 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
926 19 23309152 . T C 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
927 19 23383229 . C G 3.54 . DP=2;AF1=0.5;CI95=0.5,0.5;DP4=0,1,0,1;MQ=37;FQ=3.54;PV4=1,1,1,1 GT:PL:GQ 0/1:31,0,31:29
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
928 19 23399342 . T C 6.2 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:35,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
929 19 23418245 . G T 40 . DP=5;AF1=0.5016;CI95=0.5,0.5;DP4=1,0,1,3;MQ=37;FQ=-6.18;PV4=0.4,0.014,1,0.043 GT:PL:GQ 0/1:70,0,22:25
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
930 19 23418278 . T A 88.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,3,3;MQ=37;FQ=-45 GT:PL:GQ 1/1:121,18,0:33
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
931 19 23418327 . A G 43.1 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,2,4;MQ=37;FQ=-45 GT:PL:GQ 1/1:76,18,0:33
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
932 19 23418353 . G C 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,1;MQ=37;FQ=-36 GT:PL:GQ 1/1:100,9,0:16
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
933 19 23418485 . T C 50.1 . DP=7;AF1=1;CI95=1,1;DP4=0,0,5,2;MQ=36;FQ=-48 GT:PL:GQ 1/1:83,21,0:39
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
934 19 23418549 . G A 17.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-33 GT:PL:GQ 1/1:49,6,0:10
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
935 19 23418558 . G A 12 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-33 GT:PL:GQ 1/1:43,6,0:9
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
936 19 23476446 . G A 4.77 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 0/1:33,3,0:3
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
937 19 23750472 . TGCAG TG 112 . INDEL;DP=41;AF1=0.5;CI95=0.5,0.5;DP4=17,13,4,5;MQ=37;FQ=115;PV4=0.71,0.16,1,1 GT:PL:GQ 0/1:150,0,255:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
938 19 23750625 . A G 139 . DP=52;AF1=1;CI95=1,1;DP4=0,0,29,22;MQ=37;FQ=-181 GT:PL:GQ 1/1:172,154,0:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
939 19 23800889 . TA T 7.35 . INDEL;DP=11;AF1=0.5;CI95=0.5,0.5;DP4=5,3,1,1;MQ=37;FQ=9.94;PV4=1,0.075,1,1 GT:PL:GQ 0/1:44,0,193:45
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
940 19 24001511 . A C 3.55 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 0/1:31,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
941 19 24021577 . A G 3.55 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 0/1:31,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
942 19 24054562 . G A 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
943 19 24069383 . T A 27.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-33 GT:PL:GQ 1/1:59,6,0:10
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
944 19 24125925 . C A 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
945 19 24191462 . G A 3.54 . DP=2;AF1=0.5;CI95=0.5,0.5;DP4=1,0,1,0;MQ=37;FQ=3.54;PV4=1,1,1,1 GT:PL:GQ 0/1:31,0,31:29
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
946 19 24196752 . C G 8.44 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=32;FQ=-33 GT:PL:GQ 1/1:39,6,0:8
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
947 19 24199057 . C T 6.02 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=25;FQ=-33 GT:PL:GQ 1/1:36,6,0:6
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
948 19 24199212 . CT CTT 18.5 . INDEL;DP=9;AF1=0.5;CI95=0.5,0.5;DP4=1,1,1,1;MQ=37;FQ=18.5;PV4=1,1,1,0.027 GT:PL:GQ 0/1:56,0,56:56
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
949 19 24205962 . ACC AC 14.4 . INDEL;DP=5;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-40.5 GT:PL:GQ 1/1:53,6,0:10
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
950 19 24209339 . CT CTT 11.5 . INDEL;DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=32;FQ=-40.5 GT:PL:GQ 1/1:50,6,0:9
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
951 19 24276126 . G A 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
952 19 24297919 . C A 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
953 19 24409006 . G T 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
954 19 24434846 . C G 6.2 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:35,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
955 19 24439851 . C G 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
956 19 25085208 . C T 4.77 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 0/1:33,3,0:3
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
957 19 25088621 . A C 4.77 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 0/1:33,3,0:3
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
958 19 25152568 . AG A 13.4 . INDEL;DP=2;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-40.5 GT:PL:GQ 1/1:52,6,0:9
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
959 19 25176862 . C T 3.55 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 0/1:31,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
960 19 25202314 . G T 3.57 . DP=2;AF1=0.5048;CI95=0.5,0.5;DP4=0,1,1,0;MQ=37;FQ=-10.6;PV4=1,1,1,1 GT:PL:GQ 0/1:31,0,17:23
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
961 19 25264826 . T A 6.2 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:35,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
962 19 25568427 . A G 28 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=25;FQ=-36 GT:PL:GQ 1/1:60,9,0:16
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
963 19 25568441 . G A 89 . DP=10;AF1=1;CI95=1,1;DP4=0,0,7,3;MQ=29;FQ=-57 GT:PL:GQ 1/1:122,30,0:57
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
964 19 25568480 . A G 169 . DP=11;AF1=1;CI95=1,1;DP4=0,0,8,3;MQ=30;FQ=-60 GT:PL:GQ 1/1:202,33,0:63
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
965 19 25568513 . T A 124 . DP=9;AF1=1;CI95=1,1;DP4=0,0,6,3;MQ=28;FQ=-54 GT:PL:GQ 1/1:157,27,0:51
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
966 19 25568527 . A G 109 . DP=9;AF1=1;CI95=1,1;DP4=0,0,6,3;MQ=28;FQ=-54 GT:PL:GQ 1/1:142,27,0:51
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
967 19 25568536 . A G 13.2 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=25;FQ=-36 GT:PL:GQ 1/1:45,9,0:14
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
968 19 25581569 . G A 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
969 19 26697796 . T A 6.2 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:35,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
970 19 26728829 . AGG ATGG,AG 8.83 . INDEL;DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=33;FQ=-40.5 GT:PL:GQ 1/1:71,30,24,46,0,43:8
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
971 19 26747187 . AGG AG 14.4 . INDEL;DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=37;FQ=-40.5 GT:PL:GQ 1/1:53,6,0:10
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
972 19 26751288 . G GAC 116 . INDEL;DP=8;AF1=1;CI95=0.5,1;DP4=0,0,5,1;MQ=35;FQ=-52.5 GT:PL:GQ 1/1:156,18,0:33
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
973 19 26756358 . CA CAAA 11.8 . INDEL;DP=6;AF1=0.5;CI95=0.5,0.5;DP4=1,1,1,1;MQ=37;FQ=14.4;PV4=1,0.41,1,0.0024 GT:PL:GQ 0/1:49,0,62:51
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
974 19 26758413 . GT GTT 52.4 . INDEL;DP=6;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=37;FQ=-43.5 GT:PL:GQ 1/1:92,9,0:16
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
975 19 26764380 . C T 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-33 GT:PL:GQ 1/1:44,6,0:9
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
976 19 26765941 . AGG AGGGG 24.2 . INDEL;DP=5;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-40.5 GT:PL:GQ 1/1:63,6,0:10
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
977 19 26780556 . A AC 18.3 . INDEL;DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=32;FQ=-40.5 GT:PL:GQ 1/1:57,6,0:10
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
978 19 26787476 . G A 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
979 19 26803166 . A G 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
980 19 26803281 . G T 7.8 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 1/1:37,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
981 19 26827257 . G A 3.54 . DP=2;AF1=0.5;CI95=0.5,0.5;DP4=1,0,1,0;MQ=37;FQ=3.54;PV4=1,1,1,1 GT:PL:GQ 0/1:31,0,31:29
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
982 19 26847473 . A C 10.2 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=37;FQ=-33 GT:PL:GQ 1/1:41,6,0:8
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
983 19 26852064 . TACACACACACACACACACACACACACACACACACACACA TACACACACACACACACACACACACACACACACACACA 118 . INDEL;DP=55;AF1=0.5;CI95=0.5,0.5;DP4=8,10,4,6;MQ=37;FQ=121;PV4=1,1,1,1 GT:PL:GQ 0/1:156,0,255:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
984 19 27313337 . G A 3.41 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=37;FQ=-33 GT:PL:GQ 1/1:32,6,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
985 19 27314462 . T C 40 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,1;MQ=37;FQ=-36 GT:PL:GQ 1/1:72,9,0:16
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
986 19 27466173 . C G 3.54 . DP=2;AF1=0.5;CI95=0.5,0.5;DP4=1,0,1,0;MQ=37;FQ=3.54;PV4=1,1,1,1 GT:PL:GQ 0/1:31,0,31:29
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
987 19 28220602 . T G 222 . DP=21;AF1=1;CI95=1,1;DP4=0,0,8,13;MQ=37;FQ=-90 GT:PL:GQ 1/1:255,63,0:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
988 19 28220622 . C T 222 . DP=21;AF1=1;CI95=1,1;DP4=0,0,8,13;MQ=37;FQ=-90 GT:PL:GQ 1/1:255,63,0:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
989 19 28220668 . G A 222 . DP=13;AF1=1;CI95=1,1;DP4=0,0,5,6;MQ=36;FQ=-60 GT:PL:GQ 1/1:255,33,0:63
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
990 19 28220691 . T C 148 . DP=7;AF1=1;CI95=1,1;DP4=0,0,3,4;MQ=36;FQ=-48 GT:PL:GQ 1/1:181,21,0:39
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
991 19 28486996 . T C 4.77 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 0/1:33,3,0:3
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
992 19 28643319 . C T 3.55 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 0/1:31,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
993 19 28643329 . C T 4.77 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30 GT:PL:GQ 0/1:33,3,0:3
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
994 19 28714335 . C A 6.98 . DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30 GT:PL:GQ 1/1:36,3,0:4
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
995 19 28837706 . A T 154 . DP=13;AF1=1;CI95=1,1;DP4=0,0,3,10;MQ=25;FQ=-66 GT:PL:GQ 1/1:187,39,0:75
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
996 19 28837717 . G A 154 . DP=13;AF1=1;CI95=1,1;DP4=0,0,3,10;MQ=25;FQ=-66 GT:PL:GQ 1/1:187,39,0:75
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
997 19 28837735 . A G 154 . DP=24;AF1=1;CI95=1,1;DP4=0,0,7,14;MQ=25;FQ=-90 GT:PL:GQ 1/1:187,63,0:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
998 19 28837767 . A G,T 177 . DP=53;AF1=1;CI95=1,1;DP4=0,0,21,29;MQ=30;FQ=-175 GT:PL:GQ 1/1:210,148,0,204,125,201:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
999 19 28837787 . C T 161 . DP=66;AF1=1;CI95=1,1;DP4=0,1,30,35;MQ=31;FQ=-206;PV4=1,1,1,1 GT:PL:GQ 1/1:194,179,0:99
192a236898f5 Add test cases for SnpSift
Jim Johnson <jj@umn.edu>
parents:
diff changeset
1000 19 28837805 . A G 222 . DP=54;AF1=1;CI95=1,1;DP4=0,0,26,26;MQ=32;FQ=-184 GT:PL:GQ 1/1:255,157,0:99