4 Jul
2012
4 Jul
'12
4:28 p.m.
Hi,
we were expecting that both reads of a pair would have different quality
scores. Maybe the data below makes our problem a bit more clear.
The majority of pairs have the same quality value for both reads (see
below), despite a large difference in the CIGAR string. It is not clear
to us, why reads with a cigar string like:
*1S1M2I3M1I4M1D2M1D60M1S *have the same quality as a perfect match. We
would have expected that non-perfect matches have a lesser mapping quality.
1. Matches which are unique, and do not have any
subdominant match:
251 >= MAPQ >= 255, XT=U
2. Matches which are unique, and have subdominant matches but a
different score:
175 >= MAPQ >= 181, XT=U
3. Matches which are putatively unique (not unique, but
distinguishable by score):
119 >= MAPQ >= 127, XT=U
4. Matches which are a perfect tie:
78 >= MAPQ >= 90, XT=R.
If I understand this correctly, the cigar string does not contribute to
the mapping score? That would explain it then, though I must admit I
feel a bit uncomfortable with reads that were mapped uniquely by
splitting them in 10 parts or more (score >= 180).
How do you take care of this? Do you clip the reads manually?
*HWI-ST661:153:D0FTJACXX:7:1101:1261:74388 99
chr11
63764389 180 25M108N50M
HWI-ST661:153:D0FTJACXX:7:1101:1261:74388 147 chr11
63764583 180 75M*
HWI-ST661:153:D0FTJACXX:7:1101:1261:98650 99 chr4
88128614 255 1S73M1S
HWI-ST661:153:D0FTJACXX:7:1101:1261:98650 147 chr4
88128727 255 75M
*HWI-ST661:153:D0FTJACXX:7:1101:1261:102235 99 chr5
21883611 180 75M
HWI-ST661:153:D0FTJACXX:7:1101:1261:102235 147 chr5
21883892 180 75M*
HWI-ST661:153:D0FTJACXX:7:1101:1261:123302 163 chr5
134262601 180 75M
HWI-ST661:153:D0FTJACXX:7:1101:1261:123302 83 chr5
134262672 180 1S74M
*HWI-ST661:153:D0FTJACXX:7:1101:1261:154720 163 chr6
32827449 180 75M
HWI-ST661:153:D0FTJACXX:7:1101:1261:154720 83 chr6
32827520 180 1S43M3D31M*
HWI-ST661:153:D0FTJACXX:7:1101:1261:174904 99 chr17
46973042 180 75M
HWI-ST661:153:D0FTJACXX:7:1101:1261:174904 147 chr17
46973131 180 2S15M1D58M
*HWI-ST661:153:D0FTJACXX:7:1101:1261:188083 163 chr22
22764112 255 75M
HWI-ST661:153:D0FTJACXX:7:1101:1261:188083 83 chr22
22764366 255 75M*
HWI-ST661:153:D0FTJACXX:7:1101:1261:188990 163 chr7
127361327 180 1S1M2I3M1I4M1D2M1D60M1S
HWI-ST661:153:D0FTJACXX:7:1101:1261:188990 83 chr7
127361431 180 24M86083N51M
*HWI-ST661:153:D0FTJACXX:7:1101:1262:7502 99 chr17
40024125 180 33M804N42M
HWI-ST661:153:D0FTJACXX:7:1101:1262:7502 147 chr17
40025749 180 75M*
HWI-ST661:153:D0FTJACXX:7:1101:1262:22026 99 chr6
32611046 180 74M1S
HWI-ST661:153:D0FTJACXX:7:1101:1262:22026 147 chr6
32611141 180 75M
*HWI-ST661:153:D0FTJACXX:7:1101:1262:72904 163 chr16
33962893 180 75M
HWI-ST661:153:D0FTJACXX:7:1101:1262:72904 83 chr16
33963059 180 75M*
HWI-ST661:153:D0FTJACXX:7:1101:1262:120662 99 chr2
107314958 119 75M
HWI-ST661:153:D0FTJACXX:7:1101:1262:120662 147 chr2
107315099 119 75M
*HWI-ST661:153:D0FTJACXX:7:1101:1262:122435 145 chr1
91852782 180 55M
HWI-ST661:153:D0FTJACXX:7:1101:1262:122435 97 chr12
127650913 255 16M1D58M1S*
HWI-ST661:153:D0FTJACXX:7:1101:1262:126215 163 chr10
13375888 180 75M
HWI-ST661:153:D0FTJACXX:7:1101:1262:126215 83 chr10
13380697 180 2S73M
*HWI-ST661:153:D0FTJACXX:7:1101:1262:136701 163 chr14
50085541 255 75M
HWI-ST661:153:D0FTJACXX:7:1101:1262:136701 83 chr14
50085669 255 75M*
HWI-ST661:153:D0FTJACXX:7:1101:1262:180551 99 chr5
88047745 180 75M
HWI-ST661:153:D0FTJACXX:7:1101:1262:180551 147 chr5
88057001 180 2M1I3M2I47M
best wishes,
Matthias & Daniela
--
Matthias Barann
Institute of Clinical Molecular Biology
Christian Albrechts University Kiel
Schittenhelmstr. 12
D-24105 Kiel, Germany
m.barann(a)ikmb.uni-kiel.de
+49 - (0)431 - 597 8681 (office)