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author anton
date Wed, 11 Jun 2014 17:11:12 -0400
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##fileformat=VCFv4.1
##fileDate=20140610
##source=Dan
##reference=file:///galaxy/data/phiX/sam_index/phiX.fa
##filter="AF > .001"
##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
##FORMAT=<ID=AF,Number=.,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
##FORMAT=<ID=NC,Number=.,Type=String,Description="Nucleotide and indel counts">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	groupA	groupB
phiX174	1503	.	A	C	0	.	AC=2;AF=0.0454545454545	GT:AC:AF:NC	0:0:0:A=20,C=1,	0:2:0.0833333333333:A=22,C=2,
phiX174	1536	.	A	C	0	.	AC=3;AF=0.0545454545455	GT:AC:AF:NC	0:3:0.111111111111:A=24,C=3,	0:0:0:A=28,C=1,
phiX174	1541	.	T	G	0	.	AC=2;AF=0.0363636363636	GT:AC:AF:NC	0:2:0.0740740740741:T=25,G=2,	0:0:0:T=28,
phiX174	1553	.	A	G	0	.	AC=2;AF=0.0408163265306	GT:AC:AF:NC	0:2:0.0952380952381:A=19,C=1,G=2,	0:0:0:A=28,
phiX174	1566	.	C	G	0	.	AC=2;AF=0.0307692307692	GT:AC:AF:NC	0:0:0:C=30,T=1,	0:2:0.0571428571429:C=33,G=2,
phiX174	1572	.	T	G	0	.	AC=2;AF=0.03125	GT:AC:AF:NC	0:2:0.0625:T=30,G=2,	0:0:0:T=32,
phiX174	1574	.	G	C	0	.	AC=3;AF=0.0441176470588	GT:AC:AF:NC	0:3:0.0882352941176:C=3,G=31,	0:0:0:G=34,
phiX174	1575	.	A	C	0	.	AC=2;AF=0.0294117647059	GT:AC:AF:NC	0:2:0.0571428571429:A=33,C=2,	0:0:0:A=33,T=1,
phiX174	1577	.	A	C	0	.	AC=3;AF=0.0441176470588	GT:AC:AF:NC	0:0:0:A=35,	0:3:0.0909090909091:A=30,C=3,
phiX174	1581	.	T	G	0	.	AC=2;AF=0.0285714285714	GT:AC:AF:NC	0:2:0.0555555555556:C=1,T=34,G=2,	0:0:0:T=34,G=1,
phiX174	1591	.	A	C	0	.	AC=3;AF=0.037037037037	GT:AC:AF:NC	0:3:0.0789473684211:A=35,C=3,	0:0:0:A=43,C=1,
phiX174	1597	.	T	G	0	.	AC=2;AF=0.025641025641	GT:AC:AF:NC	0:2:0.0606060606061:T=31,G=2,	0:0:0:C=1,T=45,
phiX174	1603	.	T	G	0	.	AC=2;AF=0.0243902439024	GT:AC:AF:NC	0:2:0.0625:T=30,G=2,	0:0:0:T=50,
phiX174	1606	.	T	G	0	.	AC=2;AF=0.0243902439024	GT:AC:AF:NC	0:2:0.0666666666667:A=1,C=1,T=28,G=2,	0:0:0:T=52,
phiX174	1611	.	A	C	0	.	AC=2;AF=0.0243902439024	GT:AC:AF:NC	0:2:0.0769230769231:A=24,C=2,	0:0:0:A=56,C=1,
phiX174	1613	.	A	G	0	.	AC=2;AF=0.0240963855422	GT:AC:AF:NC	0:0:0:A=25,C=1,G=1,	0:2:0.0344827586207:A=56,G=2,
phiX174	1618	.	C	A	0	.	AC=2;AF=0.0229885057471	GT:AC:AF:NC	0:2:0.0666666666667:A=2,C=28,G=1,	0:0:0:A=1,C=57,
phiX174	1619	.	C	A	0	.	AC=2;AF=0.0229885057471	GT:AC:AF:NC	0:2:0.0666666666667:A=2,C=28,	0:0:0:C=57,
phiX174	1621	.	A	C	0	.	AC=3;AF=0.0352941176471	GT:AC:AF:NC	0:0:0:A=31,T=1,G=1,	0:3:0.0555555555556:A=51,C=3,
phiX174	1622	.	G	T	0	.	AC=2;AF=0.0224719101124	GT:AC:AF:NC	0:0:0:A=1,G=35,	0:2:0.037037037037:T=2,G=52,
phiX174	1624	.	A	G	0	.	AC=2;AF=0.0235294117647	GT:AC:AF:NC	0:2:0.0555555555556:A=34,T=1,G=2,	0:0:0:A=49,
phiX174	1627	.	T	G,C	0	.	AC=2,2;AF=0.0246913580247,0.0246913580247	GT:AC:AF:NC	0:0,0:0,0:T=37,G=1,	0:2,2:0.0454545454545,0.0454545454545:C=2,T=40,G=2,
phiX174	1630	.	T	G	0	.	AC=2;AF=0.025641025641	GT:AC:AF:NC	0:2:0.0526315789474:C=1,T=36,G=2,	0:0:0:T=40,
phiX174	1632	.	A	C	0	.	AC=2;AF=0.0246913580247	GT:AC:AF:NC	0:2:0.05:A=38,C=2,	0:0:0:A=41,
phiX174	1634	.	T	G	0	.	AC=4;AF=0.0493827160494	GT:AC:AF:NC	0:2:0.047619047619:C=1,T=40,G=2,	0:2:0.0512820512821:T=37,G=2,
phiX174	1635	.	T	G	0	.	AC=3;AF=0.0365853658537	GT:AC:AF:NC	0:3:0.0714285714286:T=39,G=3,	0:0:0:T=40,
phiX174	1639	.	G	A	0	.	AC=3;AF=0.0405405405405	GT:AC:AF:NC	0:3:0.075:A=3,T=1,G=37,	0:0:0:G=34,
phiX174	1645	.	T	G	0	.	AC=2;AF=0.027027027027	GT:AC:AF:NC	0:2:0.0425531914894:T=45,G=2,	0:0:0:T=27,G=1,
phiX174	1647	.	A	T,G,C	0	.	AC=2,2,2;AF=0.0253164556962,0.0253164556962,0.0253164556962	GT:AC:AF:NC	0:0,2,2:0,0.0384615384615,0.0384615384615:A=48,C=2,G=2,	0:2,0,0:0.0740740740741,0,0:A=25,T=2,
phiX174	1652	.	G	A	0	.	AC=2;AF=0.0240963855422	GT:AC:AF:NC	0:2:0.037037037037:A=2,G=52,	0:0:0:G=29,
phiX174	1656	.	T	G	0	.	AC=3;AF=0.0348837209302	GT:AC:AF:NC	0:3:0.0555555555556:T=51,G=3,	0:0:0:T=32,G=1,
phiX174	1658	.	A	C	0	.	AC=2;AF=0.0240963855422	GT:AC:AF:NC	0:2:0.04:A=48,C=2,	0:0:0:A=33,
phiX174	1659	.	T	G	0	.	AC=3;AF=0.0365853658537	GT:AC:AF:NC	0:3:0.0625:C=1,T=45,G=3,	0:0:0:T=34,
phiX174	1663	.	T	G	0	.	AC=4;AF=0.0454545454545	GT:AC:AF:NC	0:0:0:A=1,T=53,	0:4:0.114285714286:T=31,G=4,
phiX174	1665	.	C	A	0	.	AC=2;AF=0.0212765957447	GT:AC:AF:NC	0:2:0.0384615384615:A=2,C=50,G=1,	0:0:0:C=42,
phiX174	1670	.	G	C	0	.	AC=2;AF=0.0224719101124	GT:AC:AF:NC	0:0,2:0,0.0408163265306:A=1,C=2,T=1,G=47,	0:0,0:0,0:T=1,G=40,
phiX174	1671	.	G	T	0	.	AC=2;AF=0.0212765957447	GT:AC:AF:NC	0:2:0.0384615384615:C=1,T=2,G=50,	0:0:0:G=42,
phiX174	1672	.	A	G	0	.	AC=3;AF=0.0315789473684	GT:AC:AF:NC	0:3:0.0545454545455:A=52,G=3,	0:0:0:A=40,T=1,
phiX174	1673	.	G	T	0	.	AC=2;AF=0.0212765957447	GT:AC:AF:NC	0:2:0.0377358490566:C=1,T=2,G=51,	0:0:0:G=41,
phiX174	1674	.	G	T	0	.	AC=4;AF=0.04	GT:AC:AF:NC	0:4:0.0714285714286:T=4,G=52,	0:0:0:G=44,
phiX174	1677	.	A	C	0	.	AC=3;AF=0.031914893617	GT:AC:AF:NC	0:3:0.0566037735849:A=50,C=3,N=1,	0:0:0:A=41,
phiX174	1678	.	A	C	0	.	AC=2;AF=0.0212765957447	GT:AC:AF:NC	0:0:0:A=54,C=1,G=1,	0:2:0.05:A=38,C=2,
phiX174	1682	.	T	C	0	.	AC=2;AF=0.0229885057471	GT:AC:AF:NC	0:2:0.0408163265306:C=2,T=47,G=1,	0:0:0:C=1,T=38,
phiX174	1685	.	T	G	0	.	AC=2;AF=0.0238095238095	GT:AC:AF:NC	0:2:0.046511627907:A=1,T=41,G=2,	0:0:0:T=41,G=1,
phiX174	1686	.	A	C	0	.	AC=2;AF=0.025641025641	GT:AC:AF:NC	0:0:0:A=39,C=1,T=1,G=1,	0:2:0.0512820512821:A=37,C=2,
phiX174	1687	.	T	C	0	.	AC=2;AF=0.0243902439024	GT:AC:AF:NC	0:2:0.047619047619:C=2,T=40,	0:0:0:A=1,T=40,
phiX174	1688	.	G	C	0	.	AC=2;AF=0.0246913580247	GT:AC:AF:NC	0:2:0.05:C=2,T=1,G=38,	0:0:0:G=41,
phiX174	1689	.	A	C	0	.	AC=2;AF=0.0243902439024	GT:AC:AF:NC	0:2:0.0487804878049:A=39,C=2,T=1,G=1,	0:0:0:A=41,C=1,
phiX174	1691	.	G	C	0	.	AC=2;AF=0.025974025974	GT:AC:AF:NC	0:2:0.05:C=2,T=1,G=38,	0:0:0:G=37,
phiX174	1693	.	T	G	0	.	AC=2;AF=0.0238095238095	GT:AC:AF:NC	0:0:0:T=42,G=1,	0:2:0.047619047619:T=40,G=2,
phiX174	1695	.	A	C	0	.	AC=2;AF=0.0232558139535	GT:AC:AF:NC	0:2:0.046511627907:A=41,C=2,	0:0:0:A=43,C=1,
phiX174	1702	.	T	C	0	.	AC=2;AF=0.0246913580247	GT:AC:AF:NC	0:2:0.0512820512821:A=1,C=2,T=37,	0:0:0:C=1,T=42,
phiX174	1707	.	T	C	0	.	AC=2;AF=0.0232558139535	GT:AC:AF:NC	0:2:0.05:C=2,T=38,	0:0:0:T=46,G=1,
phiX174	1708	.	A	C	0	.	AC=2;AF=0.0238095238095	GT:AC:AF:NC	0:2:0.0526315789474:A=36,C=2,	0:0:0:A=46,C=1,G=1,
phiX174	1710	.	T	C	0	.	AC=2;AF=0.025	GT:AC:AF:NC	0:0:0:C=1,T=34,	0:2:0.0434782608696:C=2,T=44,
phiX174	1723	.	T	C	0	.	AC=2;AF=0.0243902439024	GT:AC:AF:NC	0:2:0.0588235294118:C=2,T=32,	0:0:0:T=48,
phiX174	1724	.	A	C	0	.	AC=4;AF=0.0481927710843	GT:AC:AF:NC	0:2:0.0571428571429:A=33,C=2,	0:2:0.0416666666667:A=46,C=2,
phiX174	1725	.	A	C	0	.	AC=2;AF=0.0243902439024	GT:AC:AF:NC	0:2:0.0606060606061:A=31,C=2,	0:0:0:A=49,
phiX174	1726	.	T	G	0	.	AC=3;AF=0.037037037037	GT:AC:AF:NC	0:3:0.0882352941176:T=31,G=3,	0:0:0:C=1,T=47,
phiX174	1730	.	T	G	0	.	AC=2;AF=0.027397260274	GT:AC:AF:NC	0:0:0:C=1,T=28,	0:2:0.0444444444444:T=43,G=2,
phiX174	1739	.	G	T	0	.	AC=3;AF=0.0434782608696	GT:AC:AF:NC	0:3:0.09375:T=3,G=29,	0:0:0:G=37,
phiX174	1746	.	A	C	0	.	AC=2;AF=0.0338983050847	GT:AC:AF:NC	0:2:0.0689655172414:A=27,C=2,	0:0:0:A=30,C=1,G=1,
phiX174	1749	.	T	G,C	0	.	AC=3,2;AF=0.044776119403,0.0298507462687	GT:AC:AF:NC	0:3,2:0.0857142857143,0.0571428571429:C=2,T=30,G=3,	0:0,0:0,0:T=32,G=1,
phiX174	1755	.	G	C	0	.	AC=2;AF=0.027397260274	GT:AC:AF:NC	0:2:0.05:C=2,G=38,	0:0:0:C=1,G=33,
phiX174	1756	.	A	G,C	0	.	AC=2,2;AF=0.0281690140845,0.0281690140845	GT:AC:AF:NC	0:0,2:0,0.0526315789474:A=36,C=2,T=1,G=1,	0:2,0:0.0606060606061,0:A=31,C=1,G=2,
phiX174	1761	.	A	G	0	.	AC=2;AF=0.0285714285714	GT:AC:AF:NC	0:2:0.0512820512821:A=37,C=1,G=2,	0:0:0:A=31,
phiX174	1764	.	A	C	0	.	AC=2;AF=0.0294117647059	GT:AC:AF:NC	0:2:0.05:A=38,C=2,	0:0:0:A=28,
phiX174	1766	.	A	C	0	.	AC=2;AF=0.0294117647059	GT:AC:AF:NC	0:2:0.0487804878049:A=39,C=2,	0:0:0:A=27,
phiX174	1769	.	T	G	0	.	AC=2;AF=0.03125	GT:AC:AF:NC	0:2:0.0526315789474:A=1,C=1,T=36,G=2,	0:0:0:T=26,G=1,
phiX174	1771	.	G	C	0	.	AC=2;AF=0.0298507462687	GT:AC:AF:NC	0:2:0.0526315789474:C=2,G=36,	0:0:0:G=29,
phiX174	1772	.	T	G	0	.	AC=4;AF=0.0597014925373	GT:AC:AF:NC	0:4:0.108108108108:C=1,T=33,G=4,	0:0:0:T=30,
phiX174	1774	.	A	G	0	.	AC=3;AF=0.0441176470588	GT:AC:AF:NC	0:3:0.0810810810811:A=34,G=3,	0:0:0:A=31,
phiX174	1775	.	G	A	0	.	AC=2;AF=0.030303030303	GT:AC:AF:NC	0:2:0.0571428571429:A=2,G=33,	0:0:0:G=31,
phiX174	1776	.	G	T	0	.	AC=2;AF=0.0289855072464	GT:AC:AF:NC	0:2:0.0540540540541:T=2,G=35,	0:0:0:G=32,
phiX174	1778	.	C	G	0	.	AC=2;AF=0.0289855072464	GT:AC:AF:NC	0:2:0.0526315789474:C=36,G=2,	0:0:0:C=31,
phiX174	1779	.	A	C	0	.	AC=3;AF=0.0441176470588	GT:AC:AF:NC	0:3:0.075:A=37,C=3,	0:0:0:A=28,
phiX174	1781	.	T	G	0	.	AC=5;AF=0.0714285714286	GT:AC:AF:NC	0:2:0.0487804878049:C=1,T=39,G=2,	0:3:0.103448275862:T=26,G=3,
phiX174	1782	.	T	G	0	.	AC=3;AF=0.0441176470588	GT:AC:AF:NC	0:3:0.075:T=37,G=3,	0:0:0:A=1,T=28,
phiX174	1783	.	T	C	0	.	AC=2;AF=0.0298507462687	GT:AC:AF:NC	0:2:0.0512820512821:C=2,T=37,	0:0:0:T=28,G=1,
phiX174	1788	.	G	T	0	.	AC=2;AF=0.0344827586207	GT:AC:AF:NC	0:0:0:A=1,T=1,G=29,	0:2:0.0689655172414:T=2,G=27,
phiX174	1792	.	T	G	0	.	AC=2;AF=0.0344827586207	GT:AC:AF:NC	0:2:0.0606060606061:T=31,G=2,	0:0:0:T=25,G=1,
phiX174	1802	.	A	C	0	.	AC=2;AF=0.030303030303	GT:AC:AF:NC	0:2:0.0571428571429:A=33,C=2,	0:0:0:A=31,C=1,
phiX174	1804	.	C	T	0	.	AC=2;AF=0.0294117647059	GT:AC:AF:NC	0:2:0.0588235294118:A=1,C=32,T=2,	0:0:0:C=34,
phiX174	1805	.	T	G	0	.	AC=3;AF=0.0441176470588	GT:AC:AF:NC	0:3:0.0857142857143:T=32,G=3,	0:0:0:T=33,G=1,
phiX174	1806	.	A	C	0	.	AC=2;AF=0.0289855072464	GT:AC:AF:NC	0:2:0.0571428571429:A=33,C=2,	0:0:0:A=34,G=1,
phiX174	1824	.	G	C	0	.	AC=2;AF=0.0281690140845	GT:AC:AF:NC	0:2:0.0714285714286:C=2,T=1,G=26,	0:0:0:G=43,
phiX174	1825	.	T	G	0	.	AC=2;AF=0.0281690140845	GT:AC:AF:NC	0:2:0.0689655172414:T=27,G=2,	0:0:0:T=42,G=1,
phiX174	1833	.	T	G	0	.	AC=2;AF=0.0289855072464	GT:AC:AF:NC	0:0:0:A=1,T=24,	0:2:0.0444444444444:T=43,G=2,
phiX174	1843	.	T	G	0	.	AC=2;AF=0.031746031746	GT:AC:AF:NC	0:2:0.08:A=1,T=23,G=2,	0:0:0:T=38,
phiX174	1847	.	A	C	0	.	AC=2;AF=0.0333333333333	GT:AC:AF:NC	0:2:0.0833333333333:A=22,C=2,T=1,G=1,	0:0:0:A=36,
phiX174	1854	.	T	G	0	.	AC=2;AF=0.0298507462687	GT:AC:AF:NC	0:0:0:T=26,	0:2:0.0487804878049:T=39,G=2,
phiX174	1860	.	T	G	0	.	AC=2;AF=0.0377358490566	GT:AC:AF:NC	0:0:0:A=1,T=20,	0:2:0.0606060606061:T=31,G=2,
phiX174	1863	.	C	G	0	.	AC=2;AF=0.0384615384615	GT:AC:AF:NC	0:2:0.105263157895:A=1,C=17,G=2,	0:0:0:C=33,
phiX174	1866	.	T	G	0	.	AC=2;AF=0.04	GT:AC:AF:NC	0:0:0:T=19,G=1,	0:2:0.0645161290323:T=29,G=2,
phiX174	1875	.	T	A	0	.	AC=2;AF=0.0377358490566	GT:AC:AF:NC	0:2:0.0952380952381:A=2,T=19,	0:0:0:T=32,G=1,
phiX174	1876	.	T	G	0	.	AC=3;AF=0.0588235294118	GT:AC:AF:NC	0:3:0.157894736842:C=1,T=16,G=3,	0:0:0:T=32,G=1,
phiX174	1882	.	T	G	0	.	AC=2;AF=0.0377358490566	GT:AC:AF:NC	0:2:0.105263157895:T=17,G=2,	0:0:0:T=34,
phiX174	1889	.	A	C	0	.	AC=2;AF=0.04	GT:AC:AF:NC	0:2:0.0869565217391:A=21,C=2,	0:0:0:A=27,
phiX174	1913	.	G	C	0	.	AC=2;AF=0.04	GT:AC:AF:NC	0:0:0:G=27,	0:2:0.0869565217391:C=2,G=21,
phiX174	1915	.	T	G	0	.	AC=2;AF=0.0425531914894	GT:AC:AF:NC	0:0:0:A=1,T=24,	0:2:0.0869565217391:T=21,G=2,
phiX174	1917	.	A	T	0	.	AC=2;AF=0.0444444444444	GT:AC:AF:NC	0:2,0:0.0833333333333,0:A=22,T=2,G=1,	0:0,0:0,0:A=21,G=1,
phiX174	1930	.	T	A	0	.	AC=2;AF=0.0526315789474	GT:AC:AF:NC	0:2:0.0909090909091:A=2,T=20,	0:0:0:T=16,
phiX174	1934	.	A	C	0	.	AC=2;AF=0.0512820512821	GT:AC:AF:NC	0:2:0.0952380952381:A=19,C=2,T=1,	0:0:0:A=18,C=1,
phiX174	1940	.	A	C	0	.	AC=2;AF=0.046511627907	GT:AC:AF:NC	0:2:0.0952380952381:A=19,C=2,	0:0:0:A=22,C=1,
phiX174	1942	.	T	G	0	.	AC=2;AF=0.047619047619	GT:AC:AF:NC	0:0:0:T=19,	0:2:0.0869565217391:T=21,G=2,
phiX174	1945	.	T	G	0	.	AC=3;AF=0.0769230769231	GT:AC:AF:NC	0:0:0:T=15,G=1,	0:3:0.125:T=21,G=3,
phiX174	1954	.	T	C	0	.	AC=2;AF=0.0625	GT:AC:AF:NC	0:0,0:0,0:T=12,G=1,	0:0,2:0,0.1:C=2,T=18,G=1,
phiX174	1959	.	T	G	0	.	AC=2;AF=0.0555555555556	GT:AC:AF:NC	0:2:0.153846153846:T=11,G=2,	0:0:0:T=23,
phiX174	1994	.	A	C	0	.	AC=2;AF=0.0512820512821	GT:AC:AF:NC	0:2:0.153846153846:A=11,C=2,	0:0:0:A=26,
phiX174	1998	.	A	G	0	.	AC=2;AF=0.05	GT:AC:AF:NC	0:2:0.142857142857:A=12,G=2,	0:0:0:A=26,