Bismark report for: /gscratch/srlab/sr320/data/cg/zr3534_6_R1.fastp-trim.20201202.fq.gz and /gscratch/srlab/sr320/data/cg/zr3534_6_R2.fastp-trim.20201202.fq.gz (version: v0.21.0) Bismark was run with Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/Crassostrea_gigas.oyster_v9.dna_sm.toplevel/ with the specified options: -q --score-min L,0,-0.6 -p 4 --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: 75321697 Number of paired-end alignments with a unique best hit: 46100544 Mapping efficiency: 61.2% Sequence pairs with no alignments under any condition: 20284411 Sequence pairs did not map uniquely: 8936742 Sequence pairs which were discarded because genomic sequence could not be extracted: 5798 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 11519621 ((converted) top strand) GA/CT/CT: 11534009 (complementary to (converted) top strand) GA/CT/GA: 11527937 (complementary to (converted) bottom strand) CT/GA/GA: 11513179 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 1608577636 Total methylated C's in CpG context: 21797457 Total methylated C's in CHG context: 1380274 Total methylated C's in CHH context: 5994483 Total methylated C's in Unknown context: 55865 Total unmethylated C's in CpG context: 184014825 Total unmethylated C's in CHG context: 279745904 Total unmethylated C's in CHH context: 1115644693 Total unmethylated C's in Unknown context: 4091675 C methylated in CpG context: 10.6% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 1.3% Bismark completed in 0d 7h 14m 43s