Bismark report for: /mmfs1/gscratch/scrubbed/strigg/analyses/20250731_methylseq/raw-reads/LCo_BSr2_R1.fastq.gz and /mmfs1/gscratch/scrubbed/strigg/analyses/20250731_methylseq/raw-reads/LCo_BSr2_R2.fastq.gz (version: v0.24.2)
Bismark was run with Bowtie 2 against the bisulfite genome of /mmfs1/gscratch/scrubbed/sr320/github/project-chilean-mussel/data/Mchi/ with the specified options: -q --score-min L,0,-0.8 -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:	100000000
Number of paired-end alignments with a unique best hit:	60875995
Mapping efficiency:	60.9% 
Sequence pairs with no alignments under any condition:	24043733
Sequence pairs did not map uniquely:	15080272
Sequence pairs which were discarded because genomic sequence could not be extracted:	7

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	30497743	((converted) top strand)
GA/CT/CT:	0	(complementary to (converted) top strand)
GA/CT/GA:	0	(complementary to (converted) bottom strand)
CT/GA/GA:	30378245	((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:	2661442491

Total methylated C's in CpG context:	50458999
Total methylated C's in CHG context:	9841039
Total methylated C's in CHH context:	48270635
Total methylated C's in Unknown context:	1856194

Total unmethylated C's in CpG context:	248851060
Total unmethylated C's in CHG context:	402932871
Total unmethylated C's in CHH context:	1901087887
Total unmethylated C's in Unknown context:	9879125

C methylated in CpG context:	16.9%
C methylated in CHG context:	2.4%
C methylated in CHH context:	2.5%
C methylated in Unknown context (CN or CHN):	15.8%


Bismark completed in 0d 4h 47m 58s