Contig name in SAM file

Question

[maryam.95]

Hi, This might be an obvious question... I have an SAM file looking something like this, my question is: How to you find the contig name (if it is possible). I have looked up the definitions of the header but do not quite get if there is any contig names, is it the same as the QNAME and if so do you need to decode it like the Flags?

QNAME   FLAG    RNAME   POS MAPQ    CIGAR   MRNM    MPOS    ISIZE   SEQ QUAL    OPT
@HD VN:1.0  SO:unsorted                                 
@SQ SN:1    LN:249250621                                    
@SQ SN:2    LN:243199373                                    
@SQ SN:3    LN:198022430                                    
@SQ SN:4    LN:191154276                                    
..........................................................                  
@SQ SN:GL000245.1   LN:36651                                    
@SQ SN:GL000246.1   LN:38154                                    
@SQ SN:GL000247.1   LN:36422                                    
@SQ SN:GL000248.1   LN:39786                                    
@SQ SN:GL000249.1   LN:38502                                    
@RG ID:S0143_RC SM:S0143    PU:no_index LB:exome    CN:Lab  PL:ILLUMINA                 
@PG ID:bowtie2  PN:bowtie2  VN:2.0.2                                
HISEQ:179:H9A7VADXX:1:1101:2961:2239    83  11  58711034    42  101M    =   58710857    -278    TCTGAAGTGGAGCTTCTAGTATCCCCAGGAGCGCGAAGTGAACACGGAAGGTACCTGCAGGATCCAATTGTGTCCATTGATCTCTCAGAGTGGCTGAGGNT   BFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFIFIIIIFIIFFFIIIIIIFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIFIIIIIIIFFFFFFFFFB0#B   AS:i:-1 XS:i:-36    XN:i:0  XM:i:1  XO:i:0  XG:i:0  NM:i:1  MD:Z:99A1   YS:i:0  YT:Z:CP RG:Z:S0143_RC
HISEQ:179:H9A7VADXX:1:1101:2961:2239    163 11  58710857    42  99M =   58711034    278 CACTTTACCTTTTTTGTCTATAAATTCATTTTGACCACGAGGCACCCCCGGAGCCTCGGTGAATCTGCTGTGATTTTGTAGGCTGCCGGATTCACAAAT BBBFFFFFFFFFFIIIFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFFFFFFFFBBBFBFFFFFFFFFBFFFFBBBBBFFFFFFFBFFFFFFFFB AS:i:0  XN:i:0  XM:i:0  XO:i:0  XG:i:0  NM:i:0  MD:Z:99 YS:i:-1 YT:Z:CP RG:Z:S0143_RC
HISEQ:179:H9A7VADXX:1:1101:2867:2247    83  17  67173782    42  101M    =   67173769    -114    AGTGAGAACTAAATTAAATAATGTATAGTGAGGCCAGATGTGGTGGCTCACACCTGTAATCCCAGCACTTTGAGAGGCTGAGGCGGGTGGATCACCTGAGG   BBFBFFBBBBFFFFFFFFBFBFBBBBBBFFFFFFFFBFIFFFFFFF<BFFBFBFFBIIIFIFFFFFBBFBFBFIFFFFFFF<IIFFFIFFFFB0BFFFBBB   AS:i:0  XN:i:0  XM:i:0  XO:i:0  XG:i:0  NM:i:0  MD:Z:101    YS:i:0  YT:Z:CP RG:Z:S0143_RC
HISEQ:179:H9A7VADXX:1:1101:2867:2247    163 17  67173769    42  99M =   67173782    114 CTTCAGAGGCATTAGTGAGAACTAAATTAAATAATGTATAGTGAGGCCAGATGTGGTGGCTCACACCTGTAATCCCAGCACTTTGAGAGGCTGAGGCGG BBBFFFFBFFFFFIIFFFFFIIBFFFFIFFIFIIIIIFBBBFFIFFFIFFIIFFFBFFFIFBBF<BFFB7B<<BBBBFBB<BFFFBBFFFFFFBBFBBB AS:i:0  XN:i:0  XM:i:0  XO:i:0  XG:i:0  NM:i:0  MD:Z:99 YS:i:0  YT:Z:CP RG:Z:S0143_RC
HISEQ:179:H9A7VADXX:1:1101:3056:2236    83  9   70883881    1   101M    =   70883861    -121    ACACAAAGATCAAGGTACTTTAAAAAAGCTATTCCTATTAATAACAAATCATTTTAGTTATTAATAATAAACATTAAGTAATTGACAAATATGCTTGATNC   FFFFFFFFFFFFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIFIIIIIIFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFFFFFFFFFB0#B   AS:i:-1 XS:i:-1 XN:i:0  XM:i:1  XO:i:0  XG:i:0  NM:i:1  MD:Z:99T1   YS:i:0  YT:Z:CP RG:Z:S0143_RC

[GenoMax]

This appears to be data aligned to hg19 (GRCh37) human genome. The @SQ lines are the chromosome names. Which contig names are you referring to?

Answer 1

[WouterDeCoster]

I assume you want to know to which chromosome/contig your reads are aligned. That is the RNAME. QNAME is the name of your read. Your header contains lines with SQ, indicating the chromosome names are 1, 2, 3, 4, 5, 6,... Other annotations may use chr1, chr2, chr3, chr4, chr5, chr6,...

From your example: the first two reads (a pair) are aligned to 11, the next pair to chromosome 17 and the last line to chromosome 9.