Bismark report for: ../data/raw-wgbs/107M_1.fastq.gz and ../data/raw-wgbs/107M_2.fastq.gz (version: v0.24.2) Bismark was run with Bowtie 2 against the bisulfite genome of /gscratch/scrubbed/sr320/github/project-mytilus-methylation/output/01-bismark-init/ with the specified options: -q --score-min L,0,-0.6 -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: 94606480 Number of paired-end alignments with a unique best hit: 44735943 Mapping efficiency: 47.3% Sequence pairs with no alignments under any condition: 39252393 Sequence pairs did not map uniquely: 10618144 Sequence pairs which were discarded because genomic sequence could not be extracted: 53 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 22385970 ((converted) top strand) GA/CT/CT: 6153 (complementary to (converted) top strand) GA/CT/GA: 6076 (complementary to (converted) bottom strand) CT/GA/GA: 22337691 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2094009985 Total methylated C's in CpG context: 34685592 Total methylated C's in CHG context: 9789192 Total methylated C's in CHH context: 48499355 Total methylated C's in Unknown context: 2443577 Total unmethylated C's in CpG context: 204295251 Total unmethylated C's in CHG context: 325425456 Total unmethylated C's in CHH context: 1471315139 Total unmethylated C's in Unknown context: 9298891 C methylated in CpG context: 14.5% C methylated in CHG context: 2.9% C methylated in CHH context: 3.2% C methylated in Unknown context (CN or CHN): 20.8% Bismark completed in 0d 5h 22m 34s