Bismark report for: ../data/69M_R1.fastp-trim.fq.gz and ../data/69M_R2.fastp-trim.fq.gz (version: v0.24.0)
Bismark was run with Bowtie 2 against the bisulfite genome of /home/shared/16TB_HDD_01/sr320/github/project-mytilus-methylation/data/ with the specified options: -q --score-min L,0,-1.0 -p 8 --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:	93353347
Number of paired-end alignments with a unique best hit:	55738899
Mapping efficiency:	59.7% 
Sequence pairs with no alignments under any condition:	18715079
Sequence pairs did not map uniquely:	18899369
Sequence pairs which were discarded because genomic sequence could not be extracted:	107

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	27885435	((converted) top strand)
GA/CT/CT:	0	(complementary to (converted) top strand)
GA/CT/GA:	0	(complementary to (converted) bottom strand)
CT/GA/GA:	27853357	((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:	2302063801

Total methylated C's in CpG context:	34544232
Total methylated C's in CHG context:	3654003
Total methylated C's in CHH context:	16549176
Total methylated C's in Unknown context:	437157

Total unmethylated C's in CpG context:	253318940
Total unmethylated C's in CHG context:	372392432
Total unmethylated C's in CHH context:	1621605018
Total unmethylated C's in Unknown context:	12747802

C methylated in CpG context:	12.0%
C methylated in CHG context:	1.0%
C methylated in CHH context:	1.0%
C methylated in unknown context (CN or CHN):	3.3%


Bismark completed in 0d 6h 22m 33s