Bismark report for: output/13-wgbs/trimmed/Qui3_R1.fq.gz and output/13-wgbs/trimmed/Qui3_R2.fq.gz (version: v0.25.1)
Bismark was run with Bowtie 2 against the bisulfite genome of /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/data/13-wgbs-genome/ with the specified options: -q --score-min L,0,-0.6 -p 2 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500
Option '--directional' specified (default mode): alignments to complementary strands (CTOT, CTOB) were ignored (i.e. not performed)

Final Alignment report
======================
Sequence pairs analysed in total:	41446330
Number of paired-end alignments with a unique best hit:	23803175
Mapping efficiency:	57.4% 
Sequence pairs with no alignments under any condition:	4367286
Sequence pairs did not map uniquely:	13275869
Sequence pairs which were discarded because genomic sequence could not be extracted:	2

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	11919458	((converted) top strand)
GA/CT/CT:	0	(complementary to (converted) top strand)
GA/CT/GA:	0	(complementary to (converted) bottom strand)
CT/GA/GA:	11883715	((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:	1047457619

Total methylated C's in CpG context:	26326058
Total methylated C's in CHG context:	1243346
Total methylated C's in CHH context:	5639286
Total methylated C's in Unknown context:	152156

Total unmethylated C's in CpG context:	101463337
Total unmethylated C's in CHG context:	176620425
Total unmethylated C's in CHH context:	736165167
Total unmethylated C's in Unknown context:	1009112

C methylated in CpG context:	20.6%
C methylated in CHG context:	0.7%
C methylated in CHH context:	0.8%
C methylated in Unknown context (CN or CHN):	13.1%


Bismark completed in 0d 0h 58m 18s