##fileformat=VCFv4.2
##fileDate=20200217
##source=freeBayes v1.3.1-dirty
##reference=reference.fasta
##contig=<ID=410976_pilon,length=101>
##phasing=none
##filter="AB > 0.2 & AB < 0.8 | AB < 0.01 | AB > 0.99 genotypes filtered with: QR > 0 | QA > 0 "
##filter="QUAL / DP > 0.1"
##filter="MQM / MQMR > 0.25 & MQM / MQMR < 1.75"
##filter="PAIRED > 0.05 & PAIREDR > 0.05 & PAIREDR / PAIRED < 1.75 & PAIREDR / PAIRED > 0.25 | PAIRED < 0.05 & PAIREDR < 0.05"
##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus">
##INFO=<ID=DPB,Number=1,Type=Float,Description="Total read depth per bp at the locus; bases in reads overlapping / bases in haplotype">
##INFO=<ID=AC,Number=A,Type=Integer,Description="Total number of alternate alleles in called genotypes">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##INFO=<ID=AF,Number=A,Type=Float,Description="Estimated allele frequency in the range (0,1]">
##INFO=<ID=RO,Number=1,Type=Integer,Description="Count of full observations of the reference haplotype.">
##INFO=<ID=AO,Number=A,Type=Integer,Description="Count of full observations of this alternate haplotype.">
##INFO=<ID=PRO,Number=1,Type=Float,Description="Reference allele observation count, with partial observations recorded fractionally">
##INFO=<ID=PAO,Number=A,Type=Float,Description="Alternate allele observations, with partial observations recorded fractionally">
##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred">
##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred">
##INFO=<ID=PQR,Number=1,Type=Float,Description="Reference allele quality sum in phred for partial observations">
##INFO=<ID=PQA,Number=A,Type=Float,Description="Alternate allele quality sum in phred for partial observations">
##INFO=<ID=SRF,Number=1,Type=Integer,Description="Number of reference observations on the forward strand">
##INFO=<ID=SRR,Number=1,Type=Integer,Description="Number of reference observations on the reverse strand">
##INFO=<ID=SAF,Number=A,Type=Integer,Description="Number of alternate observations on the forward strand">
##INFO=<ID=SAR,Number=A,Type=Integer,Description="Number of alternate observations on the reverse strand">
##INFO=<ID=SRP,Number=1,Type=Float,Description="Strand balance probability for the reference allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SRF and SRR given E(SRF/SRR) ~ 0.5, derived using Hoeffding's inequality">
##INFO=<ID=SAP,Number=A,Type=Float,Description="Strand balance probability for the alternate allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SAF and SAR given E(SAF/SAR) ~ 0.5, derived using Hoeffding's inequality">
##INFO=<ID=AB,Number=A,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous">
##INFO=<ID=ABP,Number=A,Type=Float,Description="Allele balance probability at heterozygous sites: Phred-scaled upper-bounds estimate of the probability of observing the deviation between ABR and ABA given E(ABR/ABA) ~ 0.5, derived using Hoeffding's inequality">
##INFO=<ID=RUN,Number=A,Type=Integer,Description="Run length: the number of consecutive repeats of the alternate allele in the reference genome">
##INFO=<ID=RPP,Number=A,Type=Float,Description="Read Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality">
##INFO=<ID=RPPR,Number=1,Type=Float,Description="Read Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality">
##INFO=<ID=RPL,Number=A,Type=Float,Description="Reads Placed Left: number of reads supporting the alternate balanced to the left (5') of the alternate allele">
##INFO=<ID=RPR,Number=A,Type=Float,Description="Reads Placed Right: number of reads supporting the alternate balanced to the right (3') of the alternate allele">
##INFO=<ID=EPP,Number=A,Type=Float,Description="End Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality">
##INFO=<ID=EPPR,Number=1,Type=Float,Description="End Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality">
##INFO=<ID=DPRA,Number=A,Type=Float,Description="Alternate allele depth ratio.  Ratio between depth in samples with each called alternate allele and those without.">
##INFO=<ID=ODDS,Number=1,Type=Float,Description="The log odds ratio of the best genotype combination to the second-best.">
##INFO=<ID=GTI,Number=1,Type=Integer,Description="Number of genotyping iterations required to reach convergence or bailout.">
##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
##INFO=<ID=CIGAR,Number=A,Type=String,Description="The extended CIGAR representation of each alternate allele, with the exception that '=' is replaced by 'M' to ease VCF parsing.  Note that INDEL alleles do not have the first matched base (which is provided by default, per the spec) referred to by the CIGAR.">
##INFO=<ID=NUMALT,Number=1,Type=Integer,Description="Number of unique non-reference alleles in called genotypes at this position.">
##INFO=<ID=MEANALT,Number=A,Type=Float,Description="Mean number of unique non-reference allele observations per sample with the corresponding alternate alleles.">
##INFO=<ID=LEN,Number=A,Type=Integer,Description="allele length">
##INFO=<ID=MQM,Number=A,Type=Float,Description="Mean mapping quality of observed alternate alleles">
##INFO=<ID=MQMR,Number=1,Type=Float,Description="Mean mapping quality of observed reference alleles">
##INFO=<ID=PAIRED,Number=A,Type=Float,Description="Proportion of observed alternate alleles which are supported by properly paired read fragments">
##INFO=<ID=PAIREDR,Number=1,Type=Float,Description="Proportion of observed reference alleles which are supported by properly paired read fragments">
##INFO=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum depth in gVCF output block.">
##INFO=<ID=END,Number=1,Type=Integer,Description="Last position (inclusive) in gVCF output record.">
##INFO=<ID=technology.Illumina,Number=A,Type=Float,Description="Fraction of observations supporting the alternate observed in reads from Illumina">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality, the Phred-scaled marginal (or unconditional) probability of the called genotype">
##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Number of observation for each allele">
##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count">
##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations">
##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count">
##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations">
##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum depth in gVCF output block.">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	BRZ_1261	BRZ_1262	BRZ_1265	BRZ_1269	BRZ_1270	BRZ_1271	BRZ_1275	BRZ_1276	BRZ_1278	BRZ_1283	BRZ_1435	BRZ_1436	BRZ_1437	BRZ_1438	BRZ_1439	BRZ_1440	BRZ_1441	BRZ_1442	BRZ_1443	BRZ_1444	BRZ_1445	BRZ_1446	BRZ_1447	BRZ_1448	BRZ_1449	BRZ_1450	BRZ_1459	BRZ_1461	BRZ_1464	BRZ_1465	BRZ_1466	BRZ_1468	BRZ_1469	BRZ_1470	BRZ_1472	BRZ_1473	BRZ_1479	BRZ_1480	BRZ_1481	BRZ_1483	BRZ_1485	BRZ_1486	BRZ_1487	BRZ_1488	BRZ_1489	BRZ_1490	BRZ_1503	BRZ_1509	BRZ_1510	BRZ_1511	KEY_1155	KEY_1156	KEY_1157	KEY_1158	KEY_1159	KEY_1160	KEY_1163	KEY_1164	KEY_1165	KEY_1166	KEY_1167	KEY_1168	KEY_1169	KEY_1170	KEY_1171	KEY_1172	KEY_1173	KEY_1174	KEY_1175	KEY_1176	KEY_1177	KEY_1178	KEY_1179	KEY_1180	KEY_1181	KEY_1182	KEY_1183	KEY_1184	KEY_1185	KEY_1186	KEY_1187	KEY_1188	KEY_1189	KEY_1190	KEY_1191	KEY_1193	KEY_1370	KEY_1371	KEY_1372	KEY_1373	KEY_1374	KEY_1375	KEY_1376	KEY_1377	KEY_1378	KEY_1379	KEY_1381	KEY_1382	KEY_1383	KEY_1391	KEY_1392	KEY_1393	KEY_1396	KEY_1397	KEY_1398	KEY_1399	KEY_1403	KEY_1404	KEY_1405	KEY_1406	KEY_1407	KEY_1409	KEY_1410	KEY_1411	MRT_1299	MRT_1300	MRT_1301	MRT_1302	MRT_1303	MRT_1304	MRT_1305	MRT_1306	MRT_1307	MRT_1308	MRT_1309	MRT_1310	MRT_1315	MRT_1316	MRT_1317	MRT_1318	MRT_1319	MRT_1320	MRT_1321	MRT_1322	MRT_1323	MRT_1324	MRT_1325	MRT_1326	MRT_1327	MRT_1328	MRT_1329	MRT_1330	MRT_1331	MRT_1332	MRT_1333	MRT_1334	MRT_1335	MRT_1336	MRT_1337	MRT_1338	MRT_1339	MRT_1340	MRT_1341	MRT_1342	MRT_1343	MRT_1347	MRT_1348	MRT_1349	MRT_1350	PNS_792	PNS_793	PNS_794	PNS_795	PNS_796	PNS_797	PNS_798	PNS_799	PNS_800	PNS_801	PNS_802	PNS_803	PNS_808	PNS_809	PNS_810	PNS_811	PNS_812	PNS_813	PNS_814	PNS_815	PNS_817	PNS_818	PNS_819	PNS_821	PNS_822	PNS_823	PNS_824	PNS_825	PNS_826	PNS_827	PNS_828	PNS_829	PNS_830	PNS_831	PNS_833	PR_1038	PR_1040	PR_1041	PR_1042	PR_1043	PR_1046	PR_1047	PR_1050	PR_1051	PR_1052	PR_1053	PR_1054	PR_1055	PR_1056	PR_1057	PR_1058	PR_1060	PR_1061	PR_1062	PR_1063	PR_945	PR_946	PR_947	PR_948	PR_949	PR_950	PR_951	PR_952	PR_953	PR_954	PR_955	PR_957	PR_958	PR_960	PR_961	PR_963	PR_964	PR_965	PR_966	PR_967	PR_968	PR_971	PR_972	PR_973	PR_974	PR_975	PR_976	PR_977	PR_979	SCA_1195	SCA_1196	SCA_1197	SCA_1198	SCA_1199	SCA_1200	SCA_1201	SCA_1203	SCA_1204	SCA_1206	SCA_1208	SCA_1212	SCA_1213	SCA_1214	SCA_1216	SCA_1217	SCA_1218	SCA_1220	SCA_1221	SCA_1222	SCA_1223	SCA_1224	SCA_1225	SCA_1226	SCA_1227	SCA_1230	SCA_1231	SCA_1232	SCA_1233	SCA_1234	SCA_1239	SCA_1240	SCA_848	SCA_853	SCA_854	SCA_857	SCA_869	SCA_871	SCA_874	SCA_876	SCA_877	SCA_880	SCA_896	SCA_897	SCA_914	SCA_915	SCA_916	SCA_917	SCA_918	SCA_919	SCA_920	SCA_921	SCA_922	SCA_923	SCA_924	SCA_925	SCA_926	SCA_927	SCA_929	SCA_930	SCA_931	SCA_932	SCA_933	TX_1098	TX_1099	TX_1100	TX_1101	TX_1104	TX_1105	TX_1107	TX_1109	TX_1110	TX_1111	TX_1113	TX_1114	TX_1120	TX_1121	TX_1122	TX_1123	TX_1125	TX_1126	TX_1127	TX_1128	TX_1130	TX_1131	TX_1132	TX_1133	TX_1134	TX_1135	TX_1136	TX_1137	TX_1138	TX_1139	TX_1140	TX_1141	TX_1142	TX_1143	TX_1144	TX_1145	TX_1146	VZ_1000	VZ_1001	VZ_1002	VZ_1004	VZ_1005	VZ_1006	VZ_1007	VZ_1009	VZ_1010	VZ_1019	VZ_1020	VZ_1021	VZ_1022	VZ_1026	VZ_1027	VZ_1029	VZ_670	VZ_671	VZ_672	VZ_673	VZ_674	VZ_675	VZ_676	VZ_677	VZ_678	VZ_679	VZ_680	VZ_681	VZ_682	VZ_683	VZ_684	VZ_685	VZ_686	VZ_687	VZ_688	VZ_689	VZ_690	VZ_691	VZ_692	VZ_693	VZ_694	VZ_695	VZ_701	VZ_702	VZ_703	VZ_704	VZ_705	VZ_706	VZ_707	VZ_708	VZ_709	VZ_992	VZ_993	VZ_994	VZ_995	VZ_996	VZ_997	VZ_999
232_pilon	2036	.	C	T	67125.3	.	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1413_pilon	361	.	T	C	174664	.	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2023_pilon	8395	.	A	G	71754.7	.	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3483_pilon	7022	.	C	T	128121	.	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4234_pilon	163	.	A	G	12291.3	.	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4411_pilon	5585	.	T	G	1.47356e+06	.	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5047_pilon	16086	.	A	G	2.03408e+06	.	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6838_pilon	32743	.	T	C	53493	.	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