Bismark report for: /home/shared/16TB_HDD_01/sr320/github/project-mytilus-methylation/output/25.1-93M-cov-recovery/reads/93M_R1.fastp-trim.fq.gz and /home/shared/16TB_HDD_01/sr320/github/project-mytilus-methylation/output/25.1-93M-cov-recovery/reads/93M_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/output/22-genome-prep/ with the specified options: -q --score-min L,0,-0.6 -p 12 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500
Option '--non_directional' specified: alignments to all strands were being performed (OT, OB, CTOT, CTOB)

Final Alignment report
======================
Sequence pairs analysed in total:	91219204
Number of paired-end alignments with a unique best hit:	46820590
Mapping efficiency:	51.3% 
Sequence pairs with no alignments under any condition:	29992887
Sequence pairs did not map uniquely:	14405727
Sequence pairs which were discarded because genomic sequence could not be extracted:	42

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	23427348	((converted) top strand)
GA/CT/CT:	9212	(complementary to (converted) top strand)
GA/CT/GA:	8779	(complementary to (converted) bottom strand)
CT/GA/GA:	23375209	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	1894232195

Total methylated C's in CpG context:	25469289
Total methylated C's in CHG context:	2701527
Total methylated C's in CHH context:	13793830
Total methylated C's in Unknown context:	249763

Total unmethylated C's in CpG context:	196109623
Total unmethylated C's in CHG context:	303121205
Total unmethylated C's in CHH context:	1353036721
Total unmethylated C's in Unknown context:	5704557

C methylated in CpG context:	11.5%
C methylated in CHG context:	0.9%
C methylated in CHH context:	1.0%
C methylated in unknown context (CN or CHN):	4.2%


Bismark completed in 0d 23h 13m 16s