What Does Am And Sm Tag In Sam Format Mean?

Question

[drramki.chop]

SAM format specfication reads:

AM="The smallest template-independent mapping quality of segments in the rest"
SM=" Template-independent mapping quality"

What do they mean in a PE context?

Left alignment
Sample = Pseq_batch16_P-Pseq-0057-P-A_1
Read group = 1
----------------------
Read name = FCH7BP5ADXX:1:1108:8326:60952#0
Alignment start = 23893153 (+)
Cigar = 100M
Mapped = yes
Mapping quality = 70
----------------------
Base = T
Base phred quality = 20
----------------------
Pair start = 14:23893186 (-)
Pair is mapped = yes
Insert size = 126
Pair orientation = F1R2
----------------------
First in pair
-------------------
LB = bar
MD = 5T11A8G4T0T50A16
PG = novoalign
RG = 1
**AM = 5**
NM = 6
**SM = 5**
PQ = 361
UQ = 183
AS = 183
PU = platform
-------------------
Right alignment
Sample = Pseq_batch16_P-Pseq-0057-P-A_1
Read group = 1
----------------------
Read name = FCH7BP5ADXX:1:1108:8326:60952#0
Alignment start = 23893186 (-)
Cigar = 7S93M
Mapped = yes
Mapping quality = 70
----------------------
----------------------
Pair start = 14:23893153 (+)
Pair is mapped = yes
Insert size = -126
Pair orientation = F1R2
----------------------
Second in pair
-------------------
LB = bar
MD = 50A17A15T8
PG = novoalign
RG = 1
**AM = 5**
NM = 3
**SM = 70**
PQ = 361
UQ = 174
AS = 174
PU = platform
-------------------

Alignment start position = 14:23893153
null

Answer 1

[Devon Ryan]

SM is the maximum mapping quality of the read if it were mapped as single-end rather than paired-end. AM is the minimum of the SM scores.

[drramki.chop]

When does these measures become useful in QC?

[Devon Ryan]

If a pair of reads maps poorly together but well when considered separately, then you might be able to compare these numbers to the MAPQ to decide whether to keep an alignment or reject it from further analysis. I would think this would be mostly useful if you're interested in finding variants. Most aligners that I've used don't provide this information.