Please Help Interpret Picard Bamindexstats Results

Question

[newDNASeqer]

I have difficulty understanding the statistics generated by PiCard BamIndexStats, part of the my stats results is:

chr7_gl000195_random length= 182896 Aligned= 3135 Unaligned= 0 chr8 length= 146364022 Aligned= 1627297 Unaligned= 0 chr8_gl000196_random length= 38914 Aligned= 869 Unaligned= 0

Does this result mean that, for chr 7 and 8, 100% of the reads are aligned to the chromosomes regions? I used bwa mem to do the alignment, is it sort of too good to be true?

[Dan D]

Did you run with the LENIENT flag? I ask because Picard will discard unmapped reads if they have a MAPQ of zero.

[Dan D]

Other things that would be helpful: can you tell us your command line for Picard, and perhaps include a few lines from the BAM?

Answer 1

[always_learning]

You may have bam file and corresponding index files for that cases here !! So as I think It will always show 100% Match here !! I may be wrong but would like to see other response !! Meanwhile what about other Chromosomes also !!