File: mpileup.4.vcf

package info (click to toggle)
bcftools 1.22-1
  • links: PTS, VCS
  • area: main
  • in suites: forky, sid
  • size: 22,792 kB
  • sloc: ansic: 72,978; perl: 7,583; sh: 694; python: 595; makefile: 301
file content (97 lines) | stat: -rw-r--r-- 8,800 bytes parent folder | download | duplicates (4) 
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
 
##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##reference=file://grch37.chr20.fa.gz
##contig=<ID=1,length=249250621>
##contig=<ID=16,length=249250621>
##contig=<ID=17,length=249250621>
##contig=<ID=20,length=249250621>
##contig=<ID=21,length=249250621>
##ALT=<ID=*,Description="Represents allele(s) other than observed.">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)">
##INFO=<ID=I16,Number=16,Type=Float,Description="Auxiliary tag used for calling, see description of bcf_callret1_t in bam2bcf.h">
##INFO=<ID=QS,Number=R,Type=Float,Description="Auxiliary tag used for calling">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	sample
1	1368813	.	G	<*>	0	.	DP=1;I16=1,0,0,0,30,900,0,0,60,3600,0,0,0,0,0,0;QS=1,0;MQ0F=0	PL	0,3,30
1	1368814	.	G	<*>	0	.	DP=1;I16=1,0,0,0,28,784,0,0,60,3600,0,0,1,1,0,0;QS=1,0;MQ0F=0	PL	0,3,28
1	1368815	.	C	<*>	0	.	DP=1;I16=1,0,0,0,32,1024,0,0,60,3600,0,0,2,4,0,0;QS=1,0;MQ0F=0	PL	0,3,32
1	1368816	.	C	<*>	0	.	DP=1;I16=1,0,0,0,24,576,0,0,60,3600,0,0,3,9,0,0;QS=1,0;MQ0F=0	PL	0,3,24
1	1368817	.	C	<*>	0	.	DP=1;I16=1,0,0,0,25,625,0,0,60,3600,0,0,4,16,0,0;QS=1,0;MQ0F=0	PL	0,3,25
1	1368818	.	T	<*>	0	.	DP=1;I16=1,0,0,0,35,1225,0,0,60,3600,0,0,5,25,0,0;QS=1,0;MQ0F=0	PL	0,3,35
1	1368819	.	C	<*>	0	.	DP=1;I16=1,0,0,0,35,1225,0,0,60,3600,0,0,6,36,0,0;QS=1,0;MQ0F=0	PL	0,3,35
1	1368820	.	A	<*>	0	.	DP=1;I16=1,0,0,0,35,1225,0,0,60,3600,0,0,7,49,0,0;QS=1,0;MQ0F=0	PL	0,3,35
1	1368821	.	C	<*>	0	.	DP=1;I16=1,0,0,0,35,1225,0,0,60,3600,0,0,8,64,0,0;QS=1,0;MQ0F=0	PL	0,3,35
1	1368822	.	T	<*>	0	.	DP=1;I16=1,0,0,0,34,1156,0,0,60,3600,0,0,9,81,0,0;QS=1,0;MQ0F=0	PL	0,3,34
1	1368823	.	T	<*>	0	.	DP=1;I16=1,0,0,0,32,1024,0,0,60,3600,0,0,10,100,0,0;QS=1,0;MQ0F=0	PL	0,3,32
1	1368824	.	T	<*>	0	.	DP=1;I16=1,0,0,0,32,1024,0,0,60,3600,0,0,11,121,0,0;QS=1,0;MQ0F=0	PL	0,3,32
1	1368825	.	C	<*>	0	.	DP=1;I16=1,0,0,0,35,1225,0,0,60,3600,0,0,12,144,0,0;QS=1,0;MQ0F=0	PL	0,3,35
1	1368826	.	A	<*>	0	.	DP=1;I16=1,0,0,0,35,1225,0,0,60,3600,0,0,13,169,0,0;QS=1,0;MQ0F=0	PL	0,3,35
1	1368827	.	T	<*>	0	.	DP=1;I16=1,0,0,0,33,1089,0,0,60,3600,0,0,14,196,0,0;QS=1,0;MQ0F=0	PL	0,3,33
1	1368828	.	G	<*>	0	.	DP=1;I16=1,0,0,0,35,1225,0,0,60,3600,0,0,15,225,0,0;QS=1,0;MQ0F=0	PL	0,3,35
1	1368829	.	T	<*>	0	.	DP=1;I16=1,0,0,0,32,1024,0,0,60,3600,0,0,16,256,0,0;QS=1,0;MQ0F=0	PL	0,3,32
1	1368830	.	T	<*>	0	.	DP=1;I16=1,0,0,0,32,1024,0,0,60,3600,0,0,17,289,0,0;QS=1,0;MQ0F=0	PL	0,3,32
1	1368831	.	C	<*>	0	.	DP=1;I16=1,0,0,0,35,1225,0,0,60,3600,0,0,18,324,0,0;QS=1,0;MQ0F=0	PL	0,3,35
1	1368832	.	T	<*>	0	.	DP=1;I16=1,0,0,0,34,1156,0,0,60,3600,0,0,19,361,0,0;QS=1,0;MQ0F=0	PL	0,3,34
1	1368833	.	T	<*>	0	.	DP=1;I16=0,1,0,0,13,169,0,0,60,3600,0,0,3,9,0,0;QS=1,0;MQ0F=0	PL	0,3,13
1	1368833	.	TAAAAAAAAAAAAAAAA	TAAAAAAAAAAAAAA	0	.	DP=2;I16=0,1,1,0,10,100,30,900,60,3600,60,3600,3,9,25,625;QS=0.5,0.5	PL	6,0,6
1	1368834	.	A	<*>	0	.	DP=1;I16=1,0,0,0,33,1089,0,0,60,3600,0,0,21,441,0,0;QS=1,0;MQ0F=0	PL	0,3,33
1	1368835	.	G	<*>	0	.	DP=1;I16=1,0,0,0,35,1225,0,0,60,3600,0,0,22,484,0,0;QS=1,0;MQ0F=0	PL	0,3,35
20	68836	.	A	<*>	0	.	DP=1;I16=1,0,0,0,34,1156,0,0,60,3600,0,0,23,529,0,0;QS=1,0;MQ0F=0	PL	0,3,34
20	68837	.	T	<*>	0	.	DP=1;I16=1,0,0,0,33,1089,0,0,60,3600,0,0,24,576,0,0;QS=1,0;MQ0F=0	PL	0,3,33
20	68838	.	A	<*>	0	.	DP=1;I16=1,0,0,0,33,1089,0,0,60,3600,0,0,25,625,0,0;QS=1,0;MQ0F=0	PL	0,3,33
20	68839	.	T	<*>	0	.	DP=1;I16=1,0,0,0,33,1089,0,0,60,3600,0,0,25,625,0,0;QS=1,0;MQ0F=0	PL	0,3,33
20	68840	.	G	<*>	0	.	DP=1;I16=1,0,0,0,35,1225,0,0,60,3600,0,0,25,625,0,0;QS=1,0;MQ0F=0	PL	0,3,35
20	68841	.	G	<*>	0	.	DP=1;I16=1,0,0,0,33,1089,0,0,60,3600,0,0,25,625,0,0;QS=1,0;MQ0F=0	PL	0,3,33
20	68842	.	T	<*>	0	.	DP=1;I16=1,0,0,0,33,1089,0,0,60,3600,0,0,25,625,0,0;QS=1,0;MQ0F=0	PL	0,3,33
20	68843	.	G	<*>	0	.	DP=1;I16=1,0,0,0,35,1225,0,0,60,3600,0,0,25,625,0,0;QS=1,0;MQ0F=0	PL	0,3,35
20	68844	.	A	<*>	0	.	DP=1;I16=1,0,0,0,34,1156,0,0,60,3600,0,0,25,625,0,0;QS=1,0;MQ0F=0	PL	0,3,34
20	68845	.	A	<*>	0	.	DP=1;I16=1,0,0,0,33,1089,0,0,60,3600,0,0,25,625,0,0;QS=1,0;MQ0F=0	PL	0,3,33
20	68846	.	C	<*>	0	.	DP=1;I16=1,0,0,0,34,1156,0,0,60,3600,0,0,25,625,0,0;QS=1,0;MQ0F=0	PL	0,3,34
20	68847	.	A	<*>	0	.	DP=1;I16=1,0,0,0,35,1225,0,0,60,3600,0,0,25,625,0,0;QS=1,0;MQ0F=0	PL	0,3,35
20	68848	.	A	<*>	0	.	DP=1;I16=1,0,0,0,33,1089,0,0,60,3600,0,0,25,625,0,0;QS=1,0;MQ0F=0	PL	0,3,33
20	68849	.	G	<*>	0	.	DP=1;I16=1,0,0,0,35,1225,0,0,60,3600,0,0,25,625,0,0;QS=1,0;MQ0F=0	PL	0,3,35
20	68850	.	T	<*>	0	.	DP=1;I16=1,0,0,0,33,1089,0,0,60,3600,0,0,25,625,0,0;QS=1,0;MQ0F=0	PL	0,3,33
20	68851	.	C	<*>	0	.	DP=1;I16=1,0,0,0,35,1225,0,0,60,3600,0,0,25,625,0,0;QS=1,0;MQ0F=0	PL	0,3,35
20	68852	.	C	<*>	0	.	DP=1;I16=1,0,0,0,24,576,0,0,60,3600,0,0,25,625,0,0;QS=1,0;MQ0F=0	PL	0,3,24
20	68853	.	A	<*>	0	.	DP=1;I16=1,0,0,0,35,1225,0,0,60,3600,0,0,25,625,0,0;QS=1,0;MQ0F=0	PL	0,3,35
20	68854	.	T	<*>	0	.	DP=1;I16=1,0,0,0,34,1156,0,0,60,3600,0,0,25,625,0,0;QS=1,0;MQ0F=0	PL	0,3,34
20	68855	.	T	<*>	0	.	DP=1;I16=1,0,0,0,32,1024,0,0,60,3600,0,0,25,625,0,0;QS=1,0;MQ0F=0	PL	0,3,32
20	68856	.	G	<*>	0	.	DP=1;I16=1,0,0,0,35,1225,0,0,60,3600,0,0,25,625,0,0;QS=1,0;MQ0F=0	PL	0,3,35
20	68857	.	A	<*>	0	.	DP=1;I16=1,0,0,0,34,1156,0,0,60,3600,0,0,25,625,0,0;QS=1,0;MQ0F=0	PL	0,3,34
20	68858	.	C	<*>	0	.	DP=1;I16=1,0,0,0,35,1225,0,0,60,3600,0,0,25,625,0,0;QS=1,0;MQ0F=0	PL	0,3,35
20	68859	.	A	<*>	0	.	DP=1;I16=1,0,0,0,35,1225,0,0,60,3600,0,0,25,625,0,0;QS=1,0;MQ0F=0	PL	0,3,35
20	68860	.	G	<*>	0	.	DP=1;I16=1,0,0,0,35,1225,0,0,60,3600,0,0,25,625,0,0;QS=1,0;MQ0F=0	PL	0,3,35
20	68861	.	T	<*>	0	.	DP=1;I16=1,0,0,0,32,1024,0,0,60,3600,0,0,25,625,0,0;QS=1,0;MQ0F=0	PL	0,3,32
20	69045	.	T	<*>	0	.	DP=1;I16=0,1,0,0,32,1024,0,0,60,3600,0,0,25,625,0,0;QS=1,0;MQ0F=0	PL	0,3,32
20	69046	.	T	<*>	0	.	DP=1;I16=0,1,0,0,32,1024,0,0,60,3600,0,0,25,625,0,0;QS=1,0;MQ0F=0	PL	0,3,32
20	69047	.	T	<*>	0	.	DP=1;I16=0,1,0,0,32,1024,0,0,60,3600,0,0,25,625,0,0;QS=1,0;MQ0F=0	PL	0,3,32
20	69048	.	A	<*>	0	.	DP=1;I16=0,1,0,0,32,1024,0,0,60,3600,0,0,25,625,0,0;QS=1,0;MQ0F=0	PL	0,3,32
20	69049	.	T	<*>	0	.	DP=1;I16=0,1,0,0,31,961,0,0,60,3600,0,0,25,625,0,0;QS=1,0;MQ0F=0	PL	0,3,31
20	69050	.	T	<*>	0	.	DP=1;I16=0,1,0,0,31,961,0,0,60,3600,0,0,25,625,0,0;QS=1,0;MQ0F=0	PL	0,3,31
20	69051	.	A	<*>	0	.	DP=1;I16=0,1,0,0,30,900,0,0,60,3600,0,0,25,625,0,0;QS=1,0;MQ0F=0	PL	0,3,30
20	69052	.	A	<*>	0	.	DP=1;I16=0,1,0,0,30,900,0,0,60,3600,0,0,24,576,0,0;QS=1,0;MQ0F=0	PL	0,3,30
20	69053	.	A	<*>	0	.	DP=1;I16=0,1,0,0,30,900,0,0,60,3600,0,0,23,529,0,0;QS=1,0;MQ0F=0	PL	0,3,30
20	69054	.	A	<*>	0	.	DP=1;I16=0,1,0,0,30,900,0,0,60,3600,0,0,22,484,0,0;QS=1,0;MQ0F=0	PL	0,3,30
20	69055	.	A	<*>	0	.	DP=1;I16=0,1,0,0,30,900,0,0,60,3600,0,0,21,441,0,0;QS=1,0;MQ0F=0	PL	0,3,30
21	69056	.	A	<*>	0	.	DP=1;I16=0,1,0,0,32,1024,0,0,60,3600,0,0,20,400,0,0;QS=1,0;MQ0F=0	PL	0,3,32
21	69057	.	T	<*>	0	.	DP=1;I16=0,1,0,0,32,1024,0,0,60,3600,0,0,19,361,0,0;QS=1,0;MQ0F=0	PL	0,3,32
21	69058	.	A	<*>	0	.	DP=1;I16=0,1,0,0,30,900,0,0,60,3600,0,0,18,324,0,0;QS=1,0;MQ0F=0	PL	0,3,30
21	69059	.	A	<*>	0	.	DP=1;I16=0,1,0,0,32,1024,0,0,60,3600,0,0,17,289,0,0;QS=1,0;MQ0F=0	PL	0,3,32
21	69060	.	T	<*>	0	.	DP=1;I16=0,1,0,0,32,1024,0,0,60,3600,0,0,16,256,0,0;QS=1,0;MQ0F=0	PL	0,3,32
21	69061	.	A	<*>	0	.	DP=1;I16=0,1,0,0,29,841,0,0,60,3600,0,0,15,225,0,0;QS=1,0;MQ0F=0	PL	0,3,29
21	69062	.	C	<*>	0	.	DP=1;I16=0,1,0,0,33,1089,0,0,60,3600,0,0,14,196,0,0;QS=1,0;MQ0F=0	PL	0,3,33
21	69063	.	T	<*>	0	.	DP=1;I16=0,1,0,0,31,961,0,0,60,3600,0,0,13,169,0,0;QS=1,0;MQ0F=0	PL	0,3,31
21	69064	.	T	<*>	0	.	DP=1;I16=0,1,0,0,33,1089,0,0,60,3600,0,0,12,144,0,0;QS=1,0;MQ0F=0	PL	0,3,33
21	69065	.	G	<*>	0	.	DP=1;I16=0,1,0,0,33,1089,0,0,60,3600,0,0,11,121,0,0;QS=1,0;MQ0F=0	PL	0,3,33
21	69066	.	C	<*>	0	.	DP=1;I16=0,1,0,0,33,1089,0,0,60,3600,0,0,10,100,0,0;QS=1,0;MQ0F=0	PL	0,3,33
21	69067	.	A	<*>	0	.	DP=1;I16=0,1,0,0,30,900,0,0,60,3600,0,0,9,81,0,0;QS=1,0;MQ0F=0	PL	0,3,30
21	69068	.	A	<*>	0	.	DP=1;I16=0,1,0,0,32,1024,0,0,60,3600,0,0,8,64,0,0;QS=1,0;MQ0F=0	PL	0,3,32
21	69069	.	T	<*>	0	.	DP=1;I16=0,1,0,0,31,961,0,0,60,3600,0,0,7,49,0,0;QS=1,0;MQ0F=0	PL	0,3,31
21	69070	.	T	<*>	0	.	DP=1;I16=0,1,0,0,33,1089,0,0,60,3600,0,0,6,36,0,0;QS=1,0;MQ0F=0	PL	0,3,33
21	69071	.	G	<*>	0	.	DP=1;I16=0,1,0,0,33,1089,0,0,60,3600,0,0,5,25,0,0;QS=1,0;MQ0F=0	PL	0,3,33
21	69072	.	A	<*>	0	.	DP=1;I16=0,1,0,0,30,900,0,0,60,3600,0,0,4,16,0,0;QS=1,0;MQ0F=0	PL	0,3,30
21	69073	.	C	<*>	0	.	DP=1;I16=0,1,0,0,30,900,0,0,60,3600,0,0,3,9,0,0;QS=1,0;MQ0F=0	PL	0,3,30
21	69074	.	T	<*>	0	.	DP=1;I16=0,1,0,0,30,900,0,0,60,3600,0,0,2,4,0,0;QS=1,0;MQ0F=0	PL	0,3,30
21	69075	.	T	<*>	0	.	DP=1;I16=0,1,0,0,28,784,0,0,60,3600,0,0,1,1,0,0;QS=1,0;MQ0F=0	PL	0,3,28
21	69076	.	A	<*>	0	.	DP=1;I16=0,1,0,0,28,784,0,0,60,3600,0,0,0,0,0,0;QS=1,0;MQ0F=0	PL	0,3,28