bowtie2 output, concordant vs. discordant reading??

[miaom]

Here are several lines from the sam file obtained from running bowtie2.
Could anybody tell me, how to tell if the mapping is concordant or discordant mapping?
Many thanks!!

#----------------------------------------------------------------------------------------------------------------------------------------------------------------
HWI-ST1148:86:C1PTAACXX:3:2316:20566:100830 81 chr2 262787705 44 100M chr1 177401969 0 GTGAGTGTAGCACAGGCGCTCACCAAAGTTCCCTTATTTGGACATCAGAGGGAATTGTCAGTCGGGTTTTTACTTAAATTAGGTAGATCTTTCTTGAATT <FBBBFBBBBB<7BBB<BBBBBFFBB<B<BFFFBFFIFFFBFFBFBFFFFFBFFFBFFFFF<F<IIFFFB0BFFBIIFFFFFIIIFFFBFFFFFFFFBBB AS:i:200 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:100 YS:i:152 YT:ZP
HWI-ST1148:86:C1PTAACXX:3:2316:20566:100830 161 chr1 177401969 44 76M24S chr2 262787705 0 GCCACACTGCTGCGTCCTGGGGCCAGCTCCTCCTCAGTCATCTCTACCCAGCCTAGGGAGCGCACAGCGAAACACTTGATCTATTAAGTTATTAATATGG BBBFFBFFFFBBFFIBFFFBFBFFIIFFIFFFFFFFFBFFIIBFFFFFIBFBBBFFIFBF7<BBBBBBBBBBBBBBBBBBBFBFFFFBBFFBBFFFFFFB AS:i:152 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:76 YS:i:200 YT:ZP
#----------------------------------------------------------------------------------------------------------------------------------------------------------------
HWI-ST1148:86:C1PTAACXX:3:2316:20514:100769 83 chrX 11366080 44 76M = 11366080 -76 GTCTTGCACAATTAATACTGTCTTTGTCACCATCCAAAACACACAACGTGTCATAAGAGGCTTTCAAACGATCAAA FFFFFFFFIIIIIFFFFIFIFIIIFIFFFIFFFIIIIFFBBFFIFFIIFFIIIIIIIIIIIFIFFFFFFFFFFBBB AS:i:152 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:76 YS:i:152 YT:Z:CP
HWI-ST1148:86:C1PTAACXX:3:2316:20514:100769 163 chrX 11366080 44 76M = 11366080 -76 GTCTTGCACAATTAATACTGTCTTTGTCACCATCCAAAACACACAACGTGTCATAAGAGGCTTTCAAACGATCAAA BBBFFFFFFFFFFIIIIIIIIIIIIIFIIIIFIIIIIIIIIIIIIIIIBFFIFIFIIFIIIIIIFIIIIFFFFFFF AS:i:152 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:76 YS:i:152 YT:Z:CP
#----------------------------------------------------------------------------------------------------------------------------------------------------------------
HWI-ST1148:86:C1PTAACXX:3:2316:20986:100818 83 chr10 109113908 1 4M1I95M = 109113853 -154 AGGGAAAAAAACCAGAACAGAAACTGGGTCCTAAGGCTCGGACTTTCCCACCCTGTTAGACTGGCAAGAAAAGAAGTGGTAACTAGTTCAGGAACCCTTG BB<<<BBBBBBBBFB<0BBFB<0<BBB<BFBBFBFFFB<<B7IIIIFFFBFFBBFFIIIFF<<FIIFIIFFFF7FIIFFBBBFBFFB<FFFFB<F<FBB< AS:i:190 XS:i:190 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:99 YS:i:190 YT:Z:CP
HWI-ST1148:86:C1PTAACXX:3:2316:20986:100818 163 chr10 109113853 1 59M1I40M = 109113908 154 GGTGTCGATGCAAACGTTCCCAACTCAAGGCAAGTAACAACCCATGGAGGTCAGGAGGGAAAAAAACCAGAACAGAAACTGGGTCCTAAGGCTCGGACTT B<BBBBFBFFBFFFIFFFFFFFFIBFFFBB<FFBFFFFFFFIFBFFFFBFFFIBBBFB7BFFFFB<BBB<'<BBBBBBBBBBB<BBBBBB00BBBB777B AS:i:190 XS:i:190 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:99 YS:i:190YT:Z:CP
#----------------------------------------------------------------------------------------------------------------------------------------------------------------
HWI-ST1148:86:C1PTAACXX:3:2316:19071:100776 99 chr1 86417046 11 100M = 86417078 107 ACTGGGGCAGAGATGACACCATGAGAAAGAGGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCGCGCG BBBFFFFFFFFFFFFFFIFFIIFBFFIIIFIFBFFFB<BFFFBFFFIIBFFIFBBFBFFFFFBBBFB<BB<BBBBBBB<BBB<BB<BBFBBBBB'07<B< AS:i:179 XS:i:138 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:29G0T65T3 YS:i:136YT:Z:CP
HWI-ST1148:86:C1PTAACXX:3:2316:19071:100776 147 chr1 86417078 11 75M = 86417046 -107 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCGCGCGTGCGCGC BBB<BBBBBBB<BBBBBBBBBBBBBBB7BBBBB<BBBBBBBBB7FFFIIFIFFFFFBIIIIIFFFFFFF7BFB<< AS:i:136 XS:i:150 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:64T3C6 YS:i:179 YT:Z:CP

[jajclement]

Hi miaom,

In sam files, you have plenty of informations related to your alignment. See samfile for the details. In particular, you have optional fields (p6-7), where you can't find anything about concordant or disconcordant alignment.

However, some fields are reserved for local use (specific to the soft for exemple): all tags beginning with 'X', 'Y', or 'Z'.
In the bowtie 2's manual, you have precisions about these tags : Bowtie 2 manual
> What you are looking for is precised in the tag YT:Z:<S>
"Value of UU indicates the read was not part of a pair. Value of CP indicates the read was part of a pair and the pair aligned concordantly. Value of DP indicates the read was part of a pair and the pair aligned discordantly. Value of UP indicates the read was part of a pair but the pair failed to aligned either concordantly or discordantly."

In your sample of reads, only the two first reads aligned disconcordantly, the others did concordantly.

I hope my explanation will be useful!
Best

Julie

[dpryan]

Please read the relevant section of the bowtie2 manual, paying particular attention to the YT field mentioned under point 12.

[miaom]

your answers help a lot!!! Thank you so much!

[miaom]

In the second reads, though I think there is something not right, the YT:Z:<S> is "CP". Should it mean align discordantly or concordantly?

#----------------------------------------------------------------------------------------------------------------------------------------------------------------
HWI-ST1148:86:C1PTAACXX:3:2316:20514:100769 83 chrX 11366080 44 76M = 11366080 -76 GTCTTGCACAATTAATACTGTCTTTGTCACCATCCAAAACACACAACGTGTCATAAGAGGCTTTCAAACGATCAAA FFFFFFFFIIIIIFFFFIFIFIIIFIFFFIFFFIIIIFFBBFFIFFIIFFIIIIIIIIIIIFIFFFFFFFFFFBBB AS:i:152 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:76 YS:i:152 YT:Z:CP
HWI-ST1148:86:C1PTAACXX:3:2316:20514:100769 163 chrX 11366080 44 76M = 11366080 -76 GTCTTGCACAATTAATACTGTCTTTGTCACCATCCAAAACACACAACGTGTCATAAGAGGCTTTCAAACGATCAAA BBBFFFFFFFFFFIIIIIIIIIIIIIFIIIIFIIIIIIIIIIIIIIIIBFFIFIFIIFIIIIIIFIIIIFFFFFFF AS:i:152 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:76 YS:i:152 YT:Z:CP
#----------------------------------------------------------------------------------------------------------------------------------------------------------------

[dpryan]

Concordantly, since bowtie2 considers alignments where one read is contained within the other to be concordant.

[wetSEQer]

Concordantly, since bowtie2 considers alignments where one read is contained within the other to be concordant.

This is not true.

[dpryan]

This is not true.

Then it's a bug in the version you're using. The documentation of the "--no-contain" option is rather explicit about this.