Entering edit mode
4.2 years ago
akshay_m180367cs
•
0
Hi, I need help to know the contents of my bam file. I read this bam file but couldnt understand the abbreviations present in it. Please help me with this.
7001448:359:C7F6GANXX:8:1207:19447:91866 83 0 21998248 60 126M 0 21998124 126 GGACAGCACTGGGAGCGTGAGGCTGCTGTGCGCTTCCAGCATGTGGGCACCTCTGTGTTCCTGTCAGTCACGGGTGAGCAGTATGGAAGCCCCATCCGTGGGCAGCATGAGGTCCACGGCATGCCC array('B', [33, 30, 29, 33, 33, 29, 40, 33, 38, 35, 36, 36, 38, 36, 38, 33, 38, 35, 38, 37, 33, 29, 38, 35, 38, 38, 35, 39, 35, 38, 34, 38, 38, 36, 34, 37, 40, 37, 38, 40, 31, 36, 38, 35, 36, 36, 38, 40, 33, 37, 38, 30, 38, 35, 39, 35, 38, 34, 34, 37, 35, 35, 39, 34, 37, 36, 38, 32, 40, 34, 34, 36, 36, 38, 35, 38, 36, 38, 40, 36, 38, 32, 34, 35, 36, 37, 34, 33, 38, 37, 37, 38, 41, 34, 34, 37, 34, 38, 35, 36, 36, 37, 40, 36, 38, 37, 34, 35, 38, 34, 36, 38, 34, 37, 40, 33, 34, 35, 37, 40, 32, 33, 33, 32, 33, 32]) [('MC', '126M'), ('BD', 'OONONNNOOOLOONONNNONNOOOOONNOONONOONONNONNNOLNNNNOOOONNNNOOOONNNONNNNNNLNNNONNONONNOONNNNLLNOOONNNOLNNONNONNONNNONNNNNNONONLNN'), ('MD', '126'), ('PG', 'MarkDuplicates.Q'), ('RG', 'tumor'), ('BI', 'RRSTSSTSSSQRRTSSTTRSSTSSTSSTSSSTRSTTTTSTTSTSQSSTTQSRSSTSRSTQSSSTTSSTTSSQSTTRTSTSSSTSRSSTSQQTTSTSSTSQSSTTSTTTRSSSTTTSSSSTTSSQSS'), ('NM', 0), ('MQ', 60), ('AS', 126), ('XS', 19)]
I got that, but what about the array mentioned in this named 'B' ??
It would appear that whatever the tool you've used to display the contents is, it's rather unusually chosen to write out the individual base qualities numerically — instead of the SAM file's native QUAL field, an ASCII-encoded string of base qualities.