Bismark report for: SRR389222_sub1_trimmed.fq.gz (version: v0.23.1)
Option '--directional' specified (default mode): alignments to complementary strands (CTOT, CTOB) were ignored (i.e. not performed)
Bismark was run with Bowtie 2 against the bisulfite genome of /mnt/lustre/agalicina/tmp/DimaTO/methylseq/work/8d/3acbd1b2f2da033dc410392bdd58da/BismarkIndex/ with the specified options: -q --score-min L,0,-0.2 --ignore-quals

Final Alignment report
======================
Sequences analysed in total:	99829
Number of alignments with a unique best hit from the different alignments:	49589
Mapping efficiency:	49.7%
Sequences with no alignments under any condition:	50240
Sequences did not map uniquely:	0
Sequences which were discarded because genomic sequence could not be extracted:	0

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	49575	((converted) top strand)
CT/GA:	14	((converted) bottom strand)
GA/CT:	0	(complementary to (converted) top strand)
GA/GA:	0	(complementary to (converted) bottom strand)

Number of alignments to (merely theoretical) complementary strands being rejected in total:	0

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	451198

Total methylated C's in CpG context:	1173
Total methylated C's in CHG context:	1178
Total methylated C's in CHH context:	1010
Total methylated C's in Unknown context:	0

Total unmethylated C's in CpG context:	125416
Total unmethylated C's in CHG context:	178381
Total unmethylated C's in CHH context:	144040
Total unmethylated C's in Unknown context:	0

C methylated in CpG context:	0.9%
C methylated in CHG context:	0.7%
C methylated in CHH context:	0.7%
Can't determine percentage of methylated Cs in Unknown context (CN or CHN) if value was 0


Bismark completed in 0d 0h 0m 18s