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  1. ##fileformat=VCFv4.1
  2. ##FILTER=<ID=PASS,Description="All filters passed">
  3. ##fileDate=20150218
  4. ##reference=ftp://ftp.1000genomes.ebi.ac.uk//vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz
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  89. ##contig=<ID=NC_007605,length=171823,assembly=b37>
  90. ##contig=<ID=hs37d5,length=35477943,assembly=b37>
  91. ##source=freeBayes v0.9.9.2 | GT values over-written with maximum likelihood state (subject to threshold) OR phylogenetic imputation
  92. ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus">
  93. ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
  94. ##source=GenomeSTRiP_v1.04
  95. ##ALT=<ID=CNV,Description="Copy number polymorphism">
  96. ##FILTER=<ID=ALIGNLENGTH,Description="GSELENGTH < 200">
  97. ##FILTER=<ID=CLUSTERSEP,Description="GSCLUSTERSEP == NA || GSCLUSTERSEP <= 2.0">
  98. ##FILTER=<ID=DUPLICATE,Description="GSDUPLICATESCORE != NA && GSDUPLICATEOVERLAP >= 0.5 && GSDUPLICATESCORE >= 0.0">
  99. ##FILTER=<ID=GTDEPTH,Description="GSM1 == NA || GSM1 <= 0.5 || GSM1 >= 2.0">
  100. ##FILTER=<ID=INBREEDINGCOEFF,Description="GLINBREEDINGCOEFF != NA && GLINBREEDINGCOEFF < -0.15">
  101. ##FILTER=<ID=NONVARIANT,Description="GSNONVARSCORE != NA && GSNONVARSCORE >= 13.0">
  102. ##FORMAT=<ID=CN,Number=1,Type=Integer,Description="Copy number genotype for imprecise events">
  103. ##FORMAT=<ID=CNL,Number=.,Type=Float,Description="Copy number likelihoods with no frequency prior">
  104. ##FORMAT=<ID=CNP,Number=.,Type=Float,Description="Copy number likelihoods">
  105. ##FORMAT=<ID=CNQ,Number=1,Type=Float,Description="Copy number genotype quality for imprecise events">
  106. ##FORMAT=<ID=GP,Number=G,Type=Float,Description="Genotype likelihoods">
  107. ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
  108. ##FORMAT=<ID=FT,Number=1,Type=String,Description="Per-sample genotype filter">
  109. ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
  110. ##INFO=<ID=END,Number=1,Type=Integer,Description="End coordinate of this variant">
  111. ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
  112. ##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral allele">
  113. ##INFO=<ID=AC,Number=A,Type=Integer,Description="Total number of alternate alleles in called genotypes">
  114. ##INFO=<ID=AF,Number=A,Type=Float,Description="Estimated allele frequency in the range (0,1]">
  115. ##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data">
  116. ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
  117. ##INFO=<ID=SAS_AF,Number=A,Type=Float,Description="Allele frequency in the SAS populations calculated from AC and AN, in the range (0,1)">
  118. ##INFO=<ID=EUR_AF,Number=A,Type=Float,Description="Allele frequency in the EUR populations calculated from AC and AN, in the range (0,1)">
  119. ##INFO=<ID=AFR_AF,Number=A,Type=Float,Description="Allele frequency in the AFR populations calculated from AC and AN, in the range (0,1)">
  120. ##INFO=<ID=AMR_AF,Number=A,Type=Float,Description="Allele frequency in the AMR populations calculated from AC and AN, in the range (0,1)">
  121. ##INFO=<ID=EAS_AF,Number=A,Type=Float,Description="Allele frequency in the EAS populations calculated from AC and AN, in the range (0,1)">
  122. ##INFO=<ID=VT,Number=.,Type=String,Description="indicates what type of variant the line represents">
  123. ##INFO=<ID=EX_TARGET,Number=0,Type=Flag,Description="indicates whether a variant is within the exon pull down target boundaries">
  124. ##INFO=<ID=MULTI_ALLELIC,Number=0,Type=Flag,Description="indicates whether a site is multi-allelic">
  125. ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth">
  126. #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00096 HG00101 HG00103 HG00105 HG00107 HG00108 HG00109 HG00112 HG00113 HG00114 HG00115 HG00116 HG00117 HG00119 HG00126 HG00129 HG00131 HG00136 HG00138 HG00139 HG00140 HG00141 HG00142 HG00143 HG00145 HG00148 HG00149 HG00151 HG00155 HG00157 HG00159 HG00160 HG00181 HG00182 HG00183 HG00185 HG00186 HG00187 HG00188 HG00189 HG00190 HG00234 HG00242 HG00243 HG00244 HG00246 HG00251 HG00252 HG00256 HG00260 HG00264 HG00265 HG00267 HG00271 HG00273 HG00277 HG00278 HG00280 HG00284 HG00290 HG00308 HG00310 HG00311 HG00321 HG00325 HG00329 HG00335 HG00336 HG00338 HG00341 HG00342 HG00345 HG00351 HG00358 HG00360 HG00366 HG00369 HG00371 HG00372 HG00375 HG00382 HG00403 HG00406 HG00409 HG00421 HG00436 HG00442 HG00445 HG00448 HG00451 HG00457 HG00463 HG00472 HG00475 HG00478 HG00500 HG00524 HG00530 HG00533 HG00536 HG00542 HG00553 HG00556 HG00559 HG00565 HG00580 HG00583 HG00589 HG00592 HG00595 HG00598 HG00607 HG00610 HG00613 HG00619 HG00622 HG00625 HG00628 HG00631 HG00634 HG00637 HG00640 HG00650 HG00653 HG00656 HG00662 HG00671 HG00674 HG00683 HG00689 HG00692 HG00698 HG00701 HG00704 HG00707 HG00728 HG00731 HG00736 HG00739 HG00742 HG00844 HG00881 HG00982 HG01028 HG01031 HG01047 HG01048 HG01051 HG01054 HG01060 HG01063 HG01066 HG01069 HG01072 HG01075 HG01079 HG01082 HG01085 HG01088 HG01094 HG01097 HG01101 HG01104 HG01107 HG01110 HG01112 HG01121 HG01124 HG01130 HG01133 HG01136 HG01139 HG01142 HG01148 HG01161 HG01164 HG01167 HG01170 HG01173 HG01176 HG01182 HG01187 HG01190 HG01197 HG01200 HG01204 HG01241 HG01247 HG01250 HG01253 HG01256 HG01259 HG01271 HG01277 HG01280 HG01286 HG01302 HG01305 HG01308 HG01311 HG01325 HG01334 HG01341 HG01344 HG01350 HG01353 HG01356 HG01359 HG01362 HG01365 HG01374 HG01377 HG01383 HG01389 HG01392 HG01395 HG01398 HG01402 HG01405 HG01412 HG01413 HG01431 HG01437 HG01440 HG01443 HG01455 HG01461 HG01464 HG01479 HG01485 HG01488 HG01491 HG01494 HG01497 HG01500 HG01503 HG01506 HG01509 HG01512 HG01515 HG01518 HG01521 HG01524 HG01527 HG01530 HG01536 HG01550 HG01556 HG01565 HG01571 HG01577 HG01583 HG01586 HG01589 HG01596 HG01603 HG01606 HG01608 HG01610 HG01615 HG01617 HG01619 HG01624 HG01625 HG01630 HG01631 HG01669 HG01672 HG01675 HG01678 HG01680 HG01682 HG01686 HG01694 HG01699 HG01700 HG01705 HG01708 HG01709 HG01747 HG01756 HG01761 HG01765 HG01767 HG01771 HG01775 HG01777 HG01781 HG01783 HG01785 HG01789 HG01791 HG01810 HG01811 HG01816 HG01840 HG01842 HG01844 HG01846 HG01849 HG01852 HG01860 HG01861 HG01864 HG01865 HG01866 HG01867 HG01872 HG01873 HG01879 HG01882 HG01885 HG01890 HG01892 HG01912 HG01914 HG01917 HG01920 HG01923 HG01926 HG01932 HG01935 HG01938 HG01941 HG01944 HG01947 HG01950 HG01953 HG01961 HG01967 HG01970 HG01974 HG01977 HG01979 HG01982 HG01986 HG01988 HG01990 HG01991 HG02002 HG02008 HG02009 HG02013 HG02014 HG02017 HG02020 HG02023 HG02026 HG02029 HG02032 HG02035 HG02040 HG02047 HG02050 HG02051 HG02053 HG02058 HG02061 HG02064 HG02067 HG02070 HG02073 HG02076 HG02079 HG02082 HG02085 HG02088 HG02090 HG02104 HG02107 HG02116 HG02122 HG02128 HG02131 HG02134 HG02137 HG02138 HG02141 HG02143 HG02146 HG02150 HG02219 HG02221 HG02224 HG02231 HG02233 HG02236 HG02238 HG02250 HG02253 HG02255 HG02259 HG02262 HG02265 HG02271 HG02274 HG02277 HG02281 HG02283 HG02284 HG02285 HG02291 HG02299 HG02304 HG02307 HG02314 HG02317 HG02323 HG02330 HG02332 HG02334 HG02343 HG02351 HG02353 HG02355 HG02356 HG02360 HG02364 HG02367 HG02371 HG02373 HG02374 HG02375 HG02379 HG02380 HG02382 HG02383 HG02384 HG02385 HG02386 HG02389 HG02390 HG02391 HG02392 HG02394 HG02395 HG02396 HG02397 HG02398 HG02399 HG02401 HG02402 HG02406 HG02407 HG02408 HG02409 HG02410 HG02420 HG02429 HG02433 HG02439 HG02442 HG02445 HG02449 HG02455 HG02461 HG02464 HG02470 HG02481 HG02484 HG02489 HG02490 HG02493 HG02496 HG02501 HG02512 HG02521 HG02536 HG02541 HG02545 HG02554 HG02557 HG02561 HG02570 HG02573 HG02582 HG02585 HG02588 HG02594 HG02597 HG02600 HG02603 HG02610 HG02613 HG02620 HG02623 HG02628 HG02634 HG02642 HG02645 HG02648 HG02651 HG02654 HG02657 HG02660 HG02666 HG02675 HG02678 HG02681 HG02684 HG02687 HG02690 HG02696 HG02699 HG02702 HG02715 HG02721 HG02724 HG02727 HG02733 HG02736 HG02756 HG02759 HG02768 HG02771 HG02774 HG02780 HG02783 HG02786 HG02789 HG02792 HG02798 HG02804 HG02807 HG02810 HG02813 HG02816 HG02819 HG02836 HG02839 HG02851 HG02854 HG02860 HG02878 HG02881 HG02884 HG02887 HG02890 HG02895 HG02923 HG02938 HG02941 HG02944 HG02947 HG02953 HG02968 HG02971 HG02973 HG02977 HG02981 HG02982 HG03006 HG03009 HG03012 HG03015 HG03018 HG03021 HG03024 HG03027 HG03039 HG03045 HG03048 HG03054 HG03057 HG03060 HG03063 HG03066 HG03069 HG03072 HG03074 HG03077 HG03078 HG03081 HG03084 HG03096 HG03100 HG03103 HG03109 HG03112 HG03115 HG03118 HG03120 HG03124 HG03127 HG03130 HG03133 HG03136 HG03139 HG03157 HG03160 HG03163 HG03166 HG03169 HG03172 HG03175 HG03190 HG03193 HG03196 HG03199 HG03202 HG03209 HG03224 HG03225 HG03228 HG03234 HG03237 HG03240 HG03246 HG03258 HG03265 HG03268 HG03271 HG03280 HG03295 HG03298 HG03301 HG03304 HG03311 HG03313 HG03343 HG03352 HG03367 HG03370 HG03376 HG03382 HG03385 HG03388 HG03391 HG03394 HG03397 HG03432 HG03433 HG03436 HG03439 HG03442 HG03445 HG03451 HG03457 HG03460 HG03469 HG03472 HG03478 HG03484 HG03490 HG03515 HG03518 HG03521 HG03538 HG03547 HG03556 HG03559 HG03565 HG03571 HG03577 HG03585 HG03593 HG03594 HG03600 HG03603 HG03615 HG03624 HG03629 HG03636 HG03644 HG03646 HG03649 HG03652 HG03660 HG03663 HG03667 HG03672 HG03679 HG03680 HG03681 HG03685 HG03686 HG03687 HG03691 HG03693 HG03694 HG03695 HG03696 HG03697 HG03702 HG03705 HG03708 HG03711 HG03713 HG03716 HG03718 HG03720 HG03727 HG03729 HG03738 HG03740 HG03742 HG03743 HG03744 HG03745 HG03746 HG03750 HG03753 HG03755 HG03767 HG03771 HG03773 HG03775 HG03777 HG03778 HG03779 HG03785 HG03786 HG03788 HG03790 HG03792 HG03800 HG03803 HG03809 HG03812 HG03815 HG03821 HG03824 HG03830 HG03833 HG03837 HG03844 HG03846 HG03848 HG03850 HG03851 HG03854 HG03856 HG03864 HG03866 HG03867 HG03869 HG03870 HG03871 HG03872 HG03875 HG03885 HG03887 HG03890 HG03896 HG03899 HG03900 HG03902 HG03905 HG03908 HG03911 HG03914 HG03917 HG03920 HG03926 HG03941 HG03943 HG03950 HG03953 HG03960 HG03963 HG03965 HG03967 HG03969 HG03971 HG03974 HG03976 HG03978 HG03985 HG03990 HG03991 HG03998 HG03999 HG04002 HG04003 HG04006 HG04015 HG04017 HG04019 HG04020 HG04022 HG04023 HG04033 HG04039 HG04056 HG04060 HG04061 HG04080 HG04093 HG04094 HG04096 HG04098 HG04100 HG04107 HG04131 HG04134 HG04140 HG04146 HG04152 HG04155 HG04158 HG04161 HG04164 HG04173 HG04176 HG04182 HG04185 HG04188 HG04194 HG04198 HG04206 HG04210 HG04211 HG04219 HG04222 HG04225 HG04229 HG04235 HG04238 HG04239 NA06984 NA06986 NA06994 NA07048 NA07051 NA07347 NA07357 NA10851 NA11829 NA11831 NA11843 NA11881 NA11893 NA11919 NA11930 NA11932 NA11992 NA11994 NA12003 NA12005 NA12043 NA12045 NA12144 NA12154 NA12155 NA12272 NA12282 NA12286 NA12340 NA12342 NA12347 NA12399 NA12413 NA12546 NA12716 NA12748 NA12750 NA12760 NA12762 NA12775 NA12777 NA12812 NA12814 NA12827 NA12829 NA12842 NA12872 NA12874 NA12889 NA18486 NA18498 NA18501 NA18504 NA18507 NA18510 NA18516 NA18519 NA18522 NA18530 NA18534 NA18536 NA18543 NA18544 NA18546 NA18548 NA18549 NA18557 NA18558 NA18559 NA18561 NA18562 NA18563 NA18572 NA18603 NA18605 NA18606 NA18608 NA18609 NA18611 NA18612 NA18613 NA18620 NA18621 NA18622 NA18623 NA18624 NA18629 NA18632 NA18633 NA18635 NA18636 NA18637 NA18638 NA18639 NA18643 NA18645 NA18647 NA18648 NA18740 NA18745 NA18747 NA18748 NA18749 NA18757 NA18853 NA18856 NA18865 NA18868 NA18871 NA18874 NA18877 NA18879 NA18908 NA18910 NA18915 NA18917 NA18923 NA18934 NA18940 NA18943 NA18944 NA18945 NA18948 NA18952 NA18953 NA18959 NA18960 NA18961 NA18962 NA18965 NA18966 NA18967 NA18970 NA18971 NA18974 NA18977 NA18982 NA18983 NA18984 NA18985 NA18986 NA18988 NA18989 NA18990 NA18994 NA18995 NA19000 NA19004 NA19005 NA19006 NA19007 NA19009 NA19012 NA19020 NA19025 NA19026 NA19027 NA19028 NA19031 NA19035 NA19041 NA19043 NA19055 NA19056 NA19058 NA19060 NA19062 NA19063 NA19066 NA19067 NA19068 NA19070 NA19072 NA19075 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