Bismark report for: ../data/272M_R1.fastp-trim.fq.gz and ../data/272M_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:	89521685
Number of paired-end alignments with a unique best hit:	54455819
Mapping efficiency:	60.8% 
Sequence pairs with no alignments under any condition:	20656242
Sequence pairs did not map uniquely:	14409624
Sequence pairs which were discarded because genomic sequence could not be extracted:	63

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	27253853	((converted) top strand)
GA/CT/CT:	0	(complementary to (converted) top strand)
GA/CT/GA:	0	(complementary to (converted) bottom strand)
CT/GA/GA:	27201903	((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:	2153931343

Total methylated C's in CpG context:	28572629
Total methylated C's in CHG context:	3301495
Total methylated C's in CHH context:	15504092
Total methylated C's in Unknown context:	399098

Total unmethylated C's in CpG context:	220109839
Total unmethylated C's in CHG context:	341255323
Total unmethylated C's in CHH context:	1545187965
Total unmethylated C's in Unknown context:	12034182

C methylated in CpG context:	11.5%
C methylated in CHG context:	1.0%
C methylated in CHH context:	1.0%
C methylated in unknown context (CN or CHN):	3.2%


Bismark completed in 0d 6h 8m 43s