Bismark report for: output/13-wgbs/trimmed/Qui2_R1.fq.gz and output/13-wgbs/trimmed/Qui2_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:	36627727
Number of paired-end alignments with a unique best hit:	20881563
Mapping efficiency:	57.0% 
Sequence pairs with no alignments under any condition:	4060145
Sequence pairs did not map uniquely:	11686019
Sequence pairs which were discarded because genomic sequence could not be extracted:	3

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	10451564	((converted) top strand)
GA/CT/CT:	0	(complementary to (converted) top strand)
GA/CT/GA:	0	(complementary to (converted) bottom strand)
CT/GA/GA:	10429996	((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:	908365821

Total methylated C's in CpG context:	24045384
Total methylated C's in CHG context:	1137125
Total methylated C's in CHH context:	5126664
Total methylated C's in Unknown context:	122314

Total unmethylated C's in CpG context:	86907051
Total unmethylated C's in CHG context:	153351251
Total unmethylated C's in CHH context:	637798346
Total unmethylated C's in Unknown context:	882366

C methylated in CpG context:	21.7%
C methylated in CHG context:	0.7%
C methylated in CHH context:	0.8%
C methylated in Unknown context (CN or CHN):	12.2%


Bismark completed in 0d 0h 52m 17s