Bismark report for: /mmfs1/gscratch/scrubbed/strigg/analyses/20250731_methylseq/raw-reads/LYa_BSr2_R1.fastq and /mmfs1/gscratch/scrubbed/strigg/analyses/20250731_methylseq/raw-reads/LYa_BSr2_R2.fastq (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 '--non_directional' specified: alignments to all strands were being performed (OT, OB, CTOT, CTOB)

Final Alignment report
======================
Sequence pairs analysed in total:	100000000
Number of paired-end alignments with a unique best hit:	60573870
Mapping efficiency:	60.6% 
Sequence pairs with no alignments under any condition:	24902286
Sequence pairs did not map uniquely:	14523844
Sequence pairs which were discarded because genomic sequence could not be extracted:	3

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	30335160	((converted) top strand)
GA/CT/CT:	11792	(complementary to (converted) top strand)
GA/CT/GA:	9978	(complementary to (converted) bottom strand)
CT/GA/GA:	30216937	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	2653520766

Total methylated C's in CpG context:	49821185
Total methylated C's in CHG context:	9868574
Total methylated C's in CHH context:	50055219
Total methylated C's in Unknown context:	1871370

Total unmethylated C's in CpG context:	246812616
Total unmethylated C's in CHG context:	404274661
Total unmethylated C's in CHH context:	1892688511
Total unmethylated C's in Unknown context:	10391655

C methylated in CpG context:	16.8%
C methylated in CHG context:	2.4%
C methylated in CHH context:	2.6%
C methylated in Unknown context (CN or CHN):	15.3%


Bismark completed in 0d 5h 8m 21s