Bismark report for: output/13-wgbs/trimmed/Qui5_R1.fq.gz and output/13-wgbs/trimmed/Qui5_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:	33149345
Number of paired-end alignments with a unique best hit:	18928762
Mapping efficiency:	57.1% 
Sequence pairs with no alignments under any condition:	3495122
Sequence pairs did not map uniquely:	10725461
Sequence pairs which were discarded because genomic sequence could not be extracted:	0

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	9473641	((converted) top strand)
GA/CT/CT:	0	(complementary to (converted) top strand)
GA/CT/GA:	0	(complementary to (converted) bottom strand)
CT/GA/GA:	9455121	((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:	852023413

Total methylated C's in CpG context:	20141665
Total methylated C's in CHG context:	1098706
Total methylated C's in CHH context:	4873801
Total methylated C's in Unknown context:	120864

Total unmethylated C's in CpG context:	86065434
Total unmethylated C's in CHG context:	144666332
Total unmethylated C's in CHH context:	595177475
Total unmethylated C's in Unknown context:	816182

C methylated in CpG context:	19.0%
C methylated in CHG context:	0.8%
C methylated in CHH context:	0.8%
C methylated in Unknown context (CN or CHN):	12.9%


Bismark completed in 0d 0h 48m 36s