reads mapped in proper pair (99/147) but mapq=0 ?

Question

[Pierre Lindenbaum]

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

[GouthamAtla]

Is it not a multi mapped read?

[Pierre Lindenbaum]

Could be, I blatted the 1st sequence:

---------------------------------------------------------------------------------------------------
browser details YourSeq          150     1   150   150 100.0%     5   -  180740198 180740347    150
browser details YourSeq          150     1   150   150 100.0%     3   -  197934503 197934652    150
browser details YourSeq          150     1   150   150 100.0%     1   +     146992    147141    150
browser details YourSeq          149     1   150   150 100.0%     4   +  120344206 120344359    154
browser details YourSeq          149     1   150   150 100.0%     1   +  243233489 243233642    154
browser details YourSeq          149     1   150   150 100.0%     1   +  222666022 222666175    154
browser details YourSeq          148     1   150   150  99.4%    19   +     212368    212517    150
browser details YourSeq          148     1   150   150  98.0%    11   +     142059    142207    149
browser details YourSeq          146     1   150   150  99.4%     7   -  128278189 128278345    157
browser details YourSeq          146     1   150   150  99.4%    16   -   90221744  90221893    150
browser details YourSeq          145     1   150   150  95.9%     1   +     682682    682827    146
browser details YourSeq          143     1   150   150  98.0%     1   +  224152894 224153048    155
browser details YourSeq          142     1   150   150  98.0%     7   -   45834042  45834191    150
browser details YourSeq          142     1   150   150  98.0%     4   -  119538519 119538668    150
browser details YourSeq          142     1   150   150  99.4%    10   -   38723425  38723575    151
browser details YourSeq          132     1   149   150  95.3%     7   +   51473634  51473794    161
browser details YourSeq          131     1   149   150  95.3%     7   -   39818221  39818388    168
browser details YourSeq          130     1   149   150  94.6%     7   +   56459438  56459599    162
browser details YourSeq          118     1   149   150  94.1%     7   -   65289482  65289689    208
browser details YourSeq          114     7   149   150  93.8%     7   +   55829219  55829373    155
browser details YourSeq          104     8   149   150  88.9%    18   -   14725111  14725269    159
(...)

[Martombo]

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)

[Pierre Lindenbaum]

it was mapped bwa 7.10

[Martombo]

Then see: What Does The Zero Mapping Quality Mean For The Bwa Mapper?

It is for general multi-mapping

[Pierre Lindenbaum]

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 :-)

[lh3]

AS:i:150 and XS:i:150 => second best hit has the same score as the best hit.