Hi,
I am using mpileup (samtools 0.1.18 (r982:295)) to look at the discordant
calls in the bam file.
I have a question about base quality scores it outputs. Below is what I get
on one of the coordinate I am troubleshooting on:
chr17 17943040 A 98
GC..,$.,....,,C.....,...,.,....,T,...,..,,..,....,....,..,.,.,.,,.,..,..,.,c...c......,..cc..,,g..^].
&(0&C&B<93D?8)<D9<D2DBB@D07D5B8&(<<B@BD8&DD0D7D5@DDDD8BD
(D<D2D<(D+DB?@I<J8&JJI.JEJJID8FF&&FFB<(@C@
]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]R]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]
I see A>C,C,c,c,c,c with quality scores, (,<,J,E,F,F i.e:
Q7,Q27,Q41,Q36,Q37,Q37 respectively.
However, in IGV I see base quality scores, of the 6 reads different as :
Q5,Q5,Q5,Q7,Q8,Q13.
Based on what I see in the bam file read entries ( from IGV list ), Q
scores are different:
Q5,Q22,Q2,Q18,Q33,Q8
These are the details from IGV read info panels:
Read name = HWI-D00522:75:HJTHTADXX:2:1105:20244:88455
Sample = SS_17
Read group = SS_17
----------------------
Location = chr17:17,943,040
Alignment start = 17,943,033 (-)
Cigar = 5S145M
Mapped = yes
Mapping quality = 60
Secondary = no
Supplementary = no
Duplicate = no
Failed QC = no
----------------------
Base = C
Base phred quality = 5
----------------------
Mate is mapped = yes
Mate start = chr17:17943021 (+)
Insert size = -156
Second in pair
Pair orientation = F1R2
----------------------
MD = 7A3A3T43T85
PG = MarkDuplicates
RG = SS_17
NM = 4
AS = 125
XS = 20
-------------------
Read name = HWI-D00522:75:HJTHTADXX:1:1207:9442:72576
Sample = SS_17
Read group = SS_17
----------------------
Location = chr17:17,943,040
Alignment start = 17,943,033 (-)
Cigar = 7S143M
Mapped = yes
Mapping quality = 60
Secondary = no
Supplementary = no
Duplicate = no
Failed QC = no
----------------------
Base = C
Base phred quality = 5
----------------------
Mate is mapped = yes
Mate start = chr17:17942905 (+)
Insert size = -270
Second in pair
Pair orientation = F1R2
----------------------
MD = 7A3A3T127
PG = MarkDuplicates
RG = SS_17
NM = 3
AS = 128
XS = 19
-------------------
Read name = HWI-D00522:75:HJTHTADXX:1:1116:6026:98077
Sample = SS_17
Read group = SS_17
----------------------
Location = chr17:17,943,040
Alignment start = 17,943,017 (-)
Cigar = 150M
Mapped = yes
Mapping quality = 60
Secondary = no
Supplementary = no
Duplicate = no
Failed QC = no
----------------------
Base = C
Base phred quality = 5
----------------------
Mate is mapped = yes
Mate start = chr17:17943014 (+)
Insert size = -152
First in pair
Pair orientation = F2R1
----------------------
MD = 23A126
PG = MarkDuplicates
RG = SS_17
NM = 1
AS = 145
XS = 19
-------------------
Read name = HWI-D00522:75:HJTHTADXX:2:1205:2127:32830
Sample = SS_17
Read group = SS_17
----------------------
Location = chr17:17,943,040
Alignment start = 17,942,893 (+)
Cigar = 150M
Mapped = yes
Mapping quality = 60
Secondary = no
Supplementary = no
Duplicate = no
Failed QC = no
----------------------
Base = C
Base phred quality = 7
----------------------
Mate is mapped = yes
Mate start = chr17:17942919 (-)
Insert size = 177
Second in pair
Pair orientation = F2R1
----------------------
MD = 101A13T3T12G7G6A2
PG = MarkDuplicates
RG = SS_17
NM = 6
AS = 122
XS = 23
-------------------
Read name = HWI-D00522:75:HJTHTADXX:2:2103:18453:22708
Sample = SS_17
Read group = SS_17
----------------------
Location = chr17:17,943,040
Alignment start = 17,942,938 (+)
Cigar = 143M7S
Mapped = yes
Mapping quality = 60
Secondary = no
Supplementary = no
Duplicate = no
Failed QC = no
----------------------
Base = C
Base phred quality = 8
----------------------
Mate is mapped = yes
Mate start = chr17:17942951 (-)
Insert size = 164
Second in pair
Pair orientation = F2R1
----------------------
MD = 73C0T8C6A2C3T4A3A2G17C1T13
PG = MarkDuplicates
RG = SS_17
NM = 11
AS = 88
XS = 0
-------------------
Read name = HWI-D00522:75:HJTHTADXX:1:2108:14591:5174
Sample = SS_17
Read group = SS_17
----------------------
Location = chr17:17,943,040
Alignment start = 17,943,022 (-)
Cigar = 150M
Mapped = yes
Mapping quality = 60
Secondary = no
Supplementary = no
Duplicate = no
Failed QC = no
----------------------
Base = C
Base phred quality = 13
----------------------
Mate is mapped = yes
Mate start = chr17:17942985 (+)
Insert size = -186
Second in pair
Pair orientation = F1R2
----------------------
MD = 13T4A7T123
PG = MarkDuplicates
RG = SS_17
NM = 3
AS = 135
XS = 0
-------------------
These are corresponding entries from bam file:
HWI-D00522:75:HJTHTADXX:1:1116:6026:98077 163 chr17 17943015
60 150M = 17943017 152
GGGGGACCCCGCGATGCCGGTCCGCACCGAGTGTCCCCCGCCGGCCGGTGCCTCCGCAGCCTCCGCGGCCTCACCCATCCCGCCGCCGCCCATCCACACCCAGCAGCCCGGCGTGGCCTCCAGCCTGCTCTACAGCGGCCCCAAGTTCCG
@@@DD:D?B?@CFA?@EG@6?FD06@FE@A<?9@;;;B>;;=@6B8-7@-8?CC?-6&07@9927>7-;9-(+2(+8A3<??B<B<B--9<5(+((((+89((+9(8<0&&50<5>BB3?B(49<(+14>:A>3((&0555&28(+4>@)
MD:Z:57T16T19A23A20T10 PG:Z:MarkDuplicates RG:Z:SS_17 NM:i:5
AS:i:125 XS:i:20
HWI-D00522:75:HJTHTADXX:1:1116:6026:98077 83 chr17 17943017
60 150M = 17943015 -152
GGGACCCCGCGATGCCGGTCCGCCCCGAGTGTCCCCCGCCGGCCGGTGCCTCCGCTGCCTCCGCGGCCTCACTCATCCCGCCGCCGCCCATCAACACCCAGCAGCCCGGCGTGGCCACCAGCCTGCTCTACAGCGGCTCCAAGTTCCGCG
82099>5585>3>7<50&9>9)0&?8?>B?<5>9>33BB@B@<B?<?<959997?8793@BB
@<88<CA>+438@BBBCCBBBB@BBCCCCBB@;5BCCCB@CCFFGGHF
;HGFFDFF>IHGCGBIHEGGIFIIHF>HAFHFD@@DD@@@ MD:Z:23A126
PG:Z:MarkDuplicates RG:Z:SS_17 NM:i:1 AS:i:145 XS:i:19
HWI-D00522:75:HJTHTADXX:2:1105:20244:88455 99 chr17 17943022
60 150M = 17943033 156
CCCGCGATGCCGGTCCGCACCGAGTGTCCCCCGCCGGCCGGTGCCTCCGCTGCCTCCGCGGCCTCACTCATCCCGCCGCCGCCCATCAACACCCAGCAGCCCGGCGTGGCCACCAGCCTGCTCTACAGCGGCTCCAAGTTCCGCGGCCAC
@CCDF6D@FHHFFDCHFHIHIGIF;FCCHGIIIHH=BBB?@@BBCCCCBBB9<A@CB@<7BBBBAC2:@C
@>CB?>B@BBBCBC@CCCCCCCBBB8ACBBB809>><B7>AABCC?BBCBB>CCCCCCC5>B3>2@C:>>AC@
@5@BB.? MD:Z:150PG:Z:MarkDuplicates RG:Z:SS_17 NM:i:0
AS:i:150 XS:i:19
HWI-D00522:75:HJTHTADXX:2:1105:20244:88455 147 chr17 17943033
60 5S145M = 17943022 -156
GGGCGGGTCCGCCCCGCGTGCCCCCCGCCGGCCGGTGCCTCCGCTGCCTCCGCGGCCTCACTCACCCCGCCGCCGCCCATCAACACCCAGCAGCCCGGCGTGGCCACCAGCCTGCTCTACAGCGGCTCCAAGTTCCGCGGCCACCAGAAG
)&&&(0)&0&&)&0&0&2&&.B99B<B<05)558A7BB>3>9B@8+<@<9BD@?DBDCC>AA<0&@BBB
<90<08DDDA>8@80+?@::(7-5@;=DD@=CCA??7FHHEAGIIE@HHA@'IHBIIHCIIIIHDHHBHHFHHDDB;A?+@
MD:Z:7A3A3T43T85 PG:Z:MarkDuplicates RG:Z:SS_17 NM:i:4
AS:i:125 XS:i:20
HWI-D00522:75:HJTHTADXX:1:1207:9442:72576 99 chr17 17942906
60 150M = 17943033 270
CCCGCCCCCACCCCGCGCGTGCGCGCCCCGGCCTCTCCCTCCCCGCCACCCTCCTCGGCTCCCGCGCGGCGGCGGCGGTTCCTCTCCCACTCCCCCCAGCCCTGGCCCCGGGGGACCCCGCGATGCCGGTCCGCACCCAGTGTCCCCCCC
@@@DDDDDFFFFFI1?8?:?AF<FAEFDC6>>B?<5>AB<<?BB57@05
?@88?9?59?05?B08080590555<9<@)58@>A:3?A3<+9<@BBB.(2<8((+2(+5&&)9@09?BB&5&)))8>&0)09&005>((2+4(+:ABB05
MD:Z:106T30G10G1 PG:Z:MarkDuplicates RG:Z:SS_17 NM:i:3
AS:i:138 XS:i:21
HWI-D00522:75:HJTHTADXX:1:1207:9442:72576 147 chr17 17943033
60 7S143M = 17942906 -270
GGTGCCGGGTCCGCCCCGGGTGCCCCCCGCCGGCCGGTGCCTCCGCTGCCTCCGCGGCCTCACTCATCCCGCCGCCGCCCATCAACACCCAGCAGCCCGGCGTGGCCACCAGCCTGCTCTACAGCGGCTCCAAGTTCCGCGGCCACCAGA
+)&&&)(0&&0))&&5&2((&)&@BB@9>DDDBB@DDBB><<DBB@
<<995<DDBBBA>>@:DC?<9DDDDBBBDDBDDDDCB@7@<DCDDDDBBDDDDDDDEFEBFEFGHIIJJJIJJIIJJIJJJJJJJIJIJIJGHHHHFFFFFCCC
MD:Z:7A3A3T127 PG:Z:MarkDuplicates RG:Z:SS_17 NM:i:3
AS:i:128 XS:i:19
HWI-D00522:75:HJTHTADXX:1:2108:14591:5174 99 chr17 17942986
60 150M = 17943022 186
CCTCTCCCACTCCCCCCAGCCCTGGCTCCGGGGGACCCCGCGATGCCGGTCCGCACCGAGTGTCCCCCGCCGGCCGGTGCCTCCGCTGCCTCCGCGGCCTCACTCATCCCGCCGCCGCCCATCAACACCCAGCAGCCCGGCGTGGCCACC
CCCFFFFFHHHHHJJJJJIJJJIIIJJJJJIJJHFDDDDDDDDDDDDDDDDDDDDDDDDD@BDEDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDCDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDBDD@DDDDDDD
MD:Z:150PG:Z:MarkDuplicates RG:Z:SS_17 NM:i:0 AS:i:150 XS:i:0
HWI-D00522:75:HJTHTADXX:1:2108:14591:5174 147 chr17 17943022
60 150M = 17942986 -186
CCCGCGATGCCGGCCCGCCCCGAGTGCCCCCCGCCGGCCGGTGCCTCCGCTGCCTCCGCGGCCTCACTCATCCCGCCGCCGCCCATCAACACCCAGCAGCCCGGCGTGGCCACCAGCCTGCTCTACAGCGGCTCCAAGTTCCGCGGCCAC
0)&+&+&&&0&5&&5&)9.8+3(2&&3BBB>9DDDDDDBDBBDDDBB@
?DDDDDDDDDDDDDDDDCDDDDDDDDDDDDDDDDDDDCDB<<<DDDDDDDDDBBDDFFFFHHHGJJJIJJIJJJJJJJJJJJJJJJJJJHHHHHFFFFF@@@
MD:Z:13T4A7T123 PG:Z:MarkDuplicates RG:Z:SS_17 NM:i:3
AS:i:135 XS:i:0
HWI-D00522:75:HJTHTADXX:2:1205:2127:32830 163 chr17 17942893
60 150M = 17942920 177
GGTGGTCGCCCCTCCCGCCCCCACCCCGCGCGTGCGCGCCCCGGCCTCTCCCTCCCCGCCACCCTCCTCGGCTCCCGCGCGGCGGCGGCGGTTCCTCTCCCCCTCCCCCCAGCCCCGGCCCCGGGGGACCCCCCGATGCCCGTCCGCCCC
@@@DDDDDHFHHFGIIAFHIIIBEHII:@
;;A,9=,96=BBB0:5<5899CC3<@BB5;B-7BB(8?(3&)8(5@B59)05<<0<5055-9&52>(:49AC0<05?BBBB&(2<B&&)0&5<&0&05&5<@B&0&&&)2>(&&+9&0(5<
MD:Z:101A13T3T12G7G6A2 PG:Z:MarkDuplicates RG:Z:SS_17 NM:i:6
AS:i:122 XS:i:23
HWI-D00522:75:HJTHTADXX:2:1205:2127:32830 83 chr17 17942920
60 150M = 17942893 -177
GCGCGTGCGCGCCCCGGCCTCTCCCTCCCCGCCACCCTCCTCGGCTCCCGCGCGGCGGCGGCGGTTCCTCTCCCACTCCCCCCAGCCCTGGCTCCGGGGGACCCCGCGATGCCGGTCCGCACCGAGTGTCCCCCGCCGGCCGGTGCCTCC
0595559>5@9DD><?8@<.>5DB90DDDBAB?2DDDBDB@BB9BBD@<DDDBDDBDBBDBDDDBADDBB<DBA8B9DDDDDDDDDDBCDBBBDBDDDDB9DDDDDDDDBDDDDDDDDBDBDDDDDBDBDDHJJJJJHHHHHFFFFFCCC
MD:Z:150PG:Z:MarkDuplicates RG:Z:SS_17 NM:i:0 AS:i:150 XS:i:23
HWI-D00522:75:HJTHTADXX:2:2103:18453:22708 163 chr17 17942938
60 143M7S = 17942952 164
CTCTCCCTCCCCGCCACCCTCCTCGGCTCCCGCGCGGCGGCGGCGGTTCCTCTCCCACTCCCCCCAGCCCTGGACCCGGGGGAACCCGCGCTGACGGACCGCCCCGTGTATCCCCCGCCGGCCGGTGACACCGCTGCCTCCGCCACCCCC
???DBDD;?ADA:8CC<C8;1:)1:6?DD;0?@@8A>@>?3:51917:0((+3++3<0+(3<;5752+8<>((((+()5;&50&2(0&00&)&&+05&&0&&)05&&)+((4:>2555>&&))&&0&((+++5.0&)(((205(&)+&5&
MD:Z:73C0T8C6A2C3T4A3A2G17C1T13 PG:Z:MarkDuplicates RG:Z:SS_17
NM:i:11 AS:i:88 XS:i:0
HWI-D00522:75:HJTHTADXX:2:2103:18453:22708 83 chr17 17942952
60 150M = 17942938 -164
CCCCCTCCTCGGCTCCCGCGCGGCGGCTGCGGTTCCTCCCCCTCCCCCCCCAGCCCTGGCTCCGGGGTACCCCGCGATGCCGTTCCGCACCGATTGTCCCCCGCCGGCCGGTGCCTCCGCTGCCTCCGCGGCCTCTCTCATCCCGCCGCC
)&>0>505)&+.>50&))&&000&8)&&50<8+(5.5)&))&&&).5)2))+(&((+()&&5&>AA>05;90&(&+&&-9-5&;;5&(20(3((80&885<<5::1:39<887:59::<==787'6>6/AA5/A=)@BA<<?ADDDD???
MD:Z:1A25G10T3A1T22G14G10G41A14 PG:Z:MarkDuplicates RG:Z:SS_17
NM:i:9 AS:i:108 XS:i:20
Can somebody tell me who is correct and why?
aparna
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