BWA MAPQ=0 with one best hit

[eoh001]

Hello
I was trying to understand the mapping quality genererated by BWA. I put all the data in xxx.sam into MySQL DB, and investigated each Tag (MAPQ, TLEN, X0, X1, SM, MQ etc) by ordering or grouping.
X0 is the number of best hits.
SM is templete-independent mapping quality.
MQ mapping quality of the mate.

I found that there were many alingnments with SM=0 and X0=1.
There is an example below.
How the alignment with one best hit goes together with SM=0?

mysql> select QNAME,FLAG,CIGAR,TLEN,MAPQ,X0,X1,XM,MD,NM,AM,SM,MQ,XT from HK11501_blood where QNAME="FCD0GULACXX:6:1106:20742:75128";[/SIZE]+--------------------------------+------+-------+------+------+------+------+------+------------+------+------+------+------+------+
| QNAME | FLAG | CIGAR | TLEN | MAPQ | X0 | X1 | XM | MD | NM | AM | SM | MQ | XT |
+--------------------------------+------+-------+------+------+------+------+------+------------+------+------+------+------+------+
| FCD0GULACXX:6:1106:20742:75128 | 163 | 90M | 241 | 0 | 1 | 2 | 3 | 21G10T19G3 | 3 | 0 | 0 | 0 | U |
| FCD0GULACXX:6:1106:20742:75128 | 83 | 90M | -241 | 0 | 1 | 2 | 1 | 7A82 | 1 | 0 | 0 | 0 | U |
+--------------------------------+------+-------+------+------+------+------+------+------------+------+------+------+------+------+

[dariober]

Hi- In the example you posted, your two reads have 3 and 1 mismatches and they also have 2 suboptimal alignment (X1 tag). These might bring the MAPQ down.

I guess the aligner is assigning to these read (example) 50% chance to come from the reported best position and 25% chance to each of the suboptimal positions. Then the MAPQ will be 0. (Not 100% sure though...)

Best
Dario

[eoh001]

Thank you..
However, I found many alignments with MAPQ > 0 under the same situation.
I wonder how to calucluate the SM of an alignment in BWA.

mysql> select QNAME,FLAG,CIGAR,TLEN,MAPQ,X0,X1,XM,MD,NM,AM,SM,MQ,XT from HK11501_blood where QNAME='FCD0GULACXX:6:1303:19123:123872';
+---------------------------------+------+-------+------+------+------+------+------+-----------+------+------+------+------+------+
| QNAME | FLAG | CIGAR | TLEN | MAPQ | X0 | X1 | XM | MD | NM | AM | SM | MQ | XT |
+---------------------------------+------+-------+------+------+------+------+------+-----------+------+------+------+------+------+
| FCD0GULACXX:6:1303:19123:123872 | 163 | 90M | 195 | 40 | 1 | 2 | 2 | 31G30G27 | 2 | 20 | 20 | 40 | U |
| FCD0GULACXX:6:1303:19123:123872 | 83 | 90M | -195 | 40 | 1 | 2 | 3 | 23G0T1G63 | 3 | 20 | 20 | 40 | U |
+---------------------------------+------+-------+------+------+------+------+------+-----------+------+------+------+------+------+