Bismark report for: ../data/242M_R1.fastp-trim.fq.gz and ../data/242M_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:	85898735
Number of paired-end alignments with a unique best hit:	51231358
Mapping efficiency:	59.6% 
Sequence pairs with no alignments under any condition:	14909255
Sequence pairs did not map uniquely:	19758122
Sequence pairs which were discarded because genomic sequence could not be extracted:	120

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	25647570	((converted) top strand)
GA/CT/CT:	0	(complementary to (converted) top strand)
GA/CT/GA:	0	(complementary to (converted) bottom strand)
CT/GA/GA:	25583668	((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:	2227176564

Total methylated C's in CpG context:	36903344
Total methylated C's in CHG context:	4027754
Total methylated C's in CHH context:	17623440
Total methylated C's in Unknown context:	482362

Total unmethylated C's in CpG context:	265741877
Total unmethylated C's in CHG context:	374199508
Total unmethylated C's in CHH context:	1528680641
Total unmethylated C's in Unknown context:	12375493

C methylated in CpG context:	12.2%
C methylated in CHG context:	1.1%
C methylated in CHH context:	1.1%
C methylated in unknown context (CN or CHN):	3.8%


Bismark completed in 0d 5h 58m 58s