# This file was produced by samtools stats (1.9+htslib-1.9) and can be plotted using plot-bamstats
# This file contains statistics for all reads.
# The command line was:  stats lig4_homo_rep1.bam
# CHK, Checksum	[2]Read Names	[3]Sequences	[4]Qualities
# CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow)
CHK	3486818e	f87155a6	590c05c8
# Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part.
SN	raw total sequences:	77460
SN	filtered sequences:	0
SN	sequences:	77460
SN	is sorted:	1
SN	1st fragments:	77460
SN	last fragments:	0
SN	reads mapped:	73067
SN	reads mapped and paired:	0	# paired-end technology bit set + both mates mapped
SN	reads unmapped:	4393
SN	reads properly paired:	0	# proper-pair bit set
SN	reads paired:	0	# paired-end technology bit set
SN	reads duplicated:	0	# PCR or optical duplicate bit set
SN	reads MQ0:	4269	# mapped and MQ=0
SN	reads QC failed:	0
SN	non-primary alignments:	121489
SN	total length:	806593589	# ignores clipping
SN	total first fragment length:	806593589	# ignores clipping
SN	total last fragment length:	0	# ignores clipping
SN	bases mapped:	795910124	# ignores clipping
SN	bases mapped (cigar):	585453223	# more accurate
SN	bases trimmed:	0
SN	bases duplicated:	0
SN	mismatches:	68001281	# from NM fields