Entering edit mode
9.4 years ago
Pierre Lindenbaum
161k
Here are two reads mapped in proper pair with bwa 7.10. (+recalibration + realign around indels). How can I explain this MAPQ= '0' ?
HWI-1KL149:89:HA4T6ADXX:2:1114:12983:47552 99 1 146992 0 150M = 147235 393 CACTTCAGCCTGGGTGACAGAGCCAGACCATGTCACAAAAAGTTAGAAAAAAAAAAGAGA
GAGGGAGAGAGACTATACACAGGCACCACCACATTTGGCTAATTTTTAAATATTCTGTAGAGACAAGGTCTTGCTAGGTTGCCCAGGCTA @B?BCEGGHFGFDCDFCBDACDEBDCCDCDCECCDCDDDDCECBCDDBACDDDCDD=?@AAAHG@DGDHDHEGFAD
CADGCGGHDFHEGHEGEEEEGAHFCBCEEDECEEECEEHEDCCHDHEGEEAF?CDDBCCC@ACEA@BCCA<@A< MC:Z:150M BD:Z:LLLNLMNPPNOONKOLOOKNNNOMNONNNNNNJNLKKLDDDMNLHMMMDDDDDDDDMNNNNMMMIMMNMLM
MNNMLMMKLKONMOLNMLNNLKNLDMMMNMLMLDDDHLDMMMLMNNKMMNNOMJMNONMMMMNNMMNNLMNMJOPNMNM MD:Z:150 RG:Z:p190 BI:Z:QQORQTNSSOSSSMSPSRMRPOSNSSQQRSQSPRNONQIIIRQRQRQRHHHHHHI
IRQOPOPPQLSPQPQPQRRRQQQNONSQOSORSORSONQPNRROSRPRPNNNQPIRQQPSRQOQPPOPRNPQPRQRQRRSRRQSQRRNQSSQOSR NM:i:0 MQ:i:0 AS:i:150 XS:i:150
HWI-1KL149:89:HA4T6ADXX:2:1114:12983:47552 147 1 147235 0 150M = 146992 -393 GGAGTTCGAGACCAGCCTGGCCAACACGGTGAAACTCTGACTCTATCAAAAATACAAAAA
TCAGCTGGGCAGTAGTGGCGTGTGCCTGTAGTCTCACCTACTCGGGAGGCTGAGGCAGGAGAATCACTTGAACCTGGGAGGTGGAGGTTG @A?BAB6>;BCGFFDA=DC@7AE@A?=CBC@B@?HBHEGCABACB<GBCEEEBCGEEEEC?BFC=DBHBFD@AFGE
GE@EEEEBCDDCDCFDACFCDFACFDCBBFCADDCDDBCDCADBCCCCFDFDDECBBAFBCFCEEEGGBGC=@? MC:Z:150M BD:Z:NNNLMMKNNNNMNNLNONMMMMLKKLMNLMMDLNNNOMMNNNMMMNMDDCLMMKLDDDLMNNNOONIMNNN
MMLLNMLLLKLOMNOKMMNNNNNKNKMMNNMMINNNMOOMMMMMNNNMNNMMNKONMMMJMOPOJOOOOMOOONMLLLL MD:Z:150 RG:Z:p190 BI:Z:SRRQRRRRRRSRRSOQSSNORRRPPQRRONSNRRPQSNQPNPQPQRQNNNPQRPR
NNNPRSRSSSSPMRRRQRROSNQQONNROPRLOPQQPORORQRPRPRRQSRRNSSNRRNRRRSRRSPRSPRQQNSRSRTTRTSSSPTSQRRQQQQ NM:i:0 MQ:i:0 AS:i:150 XS:i:150
Is it not a multi mapped read?
Could be, I blatted the 1st sequence:
how were the reads mapped?
if tophat was used, the mapping quality refers to the number of times a read maps to different locations on the genome (MAPQ==0: more than 5 mapping sites, I think)
it was mapped bwa 7.10
Then see: What Does The Zero Mapping Quality Mean For The Bwa Mapper?
It is for general multi-mapping
OK, seems to be a multi-mapped read. I expected to find a flag/property about this in the reads. I'll validate the 1st answer about this :-)
AS:i:150 and XS:i:150 => second best hit has the same score as the best hit.