Hi all ! My first post on this web site witch helped me a lot in many times before !!
I got a question about mpileup, i took an exemple from : http://samtools.sourceforge.net/pileup.shtml :
seq2 156 A 11 .$......+2AG.+2AG.+2AGGG <975;:<<<<<
If i understood right the column 4 represent the the number of reads covering the site but in reality there is not 11 but 14 reads covering in reality. I mean if you are looking for mutation like INDEL on this position after filtering by covering you could miss some interesting mutation site isn't it ?
My second question : i saw that .^] in read bases (column 5) and in all the cases it correspond of the start of the reads is it normal ? (there is no base before then why there is a quality ? )
Thanks
I got a question about mpileup, i took an exemple from : http://samtools.sourceforge.net/pileup.shtml :
seq2 156 A 11 .$......+2AG.+2AG.+2AGGG <975;:<<<<<
If i understood right the column 4 represent the the number of reads covering the site but in reality there is not 11 but 14 reads covering in reality. I mean if you are looking for mutation like INDEL on this position after filtering by covering you could miss some interesting mutation site isn't it ?
My second question : i saw that .^] in read bases (column 5) and in all the cases it correspond of the start of the reads is it normal ? (there is no base before then why there is a quality ? )
Thanks
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