I have BAM files of reads mapping to contigs assembled from those reads. I would like to get information about the amount of properly paired reads aligned to each contig.
samtools coverage --rf 2 file.bam I can get these results.
I was wondering though whether this means that the output number of reads refers to only those mapping to the same contig or does this only mean that that certain number of reads are properly paired but the mate can be aligned to some other contig (or not at all for that matter).
#rname startpos endpos numreads NODE_1_length_44838_cov_5.55007 1 44838 3193 NODE_1_length_44838_cov_5.55007 1 44838 2772
The first line is the total amount of reads mapped to NODE_1 and the second was by using the --rf 2 parameter. Does this mean that both mates of properly paired reads aligned to this contig resulting in 2772?
If not, then how could I get information about how many mate pairs both aligned to the same contig?
Thank you for your help
Thank you for your reply.