Bismark report for: /gscratch/srlab/sr320/data/cg/zr3644_11_R1.fastp-trim.20201206.fq.gz and /gscratch/srlab/sr320/data/cg/zr3644_11_R2.fastp-trim.20201206.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: 55732442 Number of paired-end alignments with a unique best hit: 34313844 Mapping efficiency: 61.6% Sequence pairs with no alignments under any condition: 14305475 Sequence pairs did not map uniquely: 7113123 Sequence pairs which were discarded because genomic sequence could not be extracted: 4587 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 8563117 ((converted) top strand) GA/CT/CT: 8590546 (complementary to (converted) top strand) GA/CT/GA: 8588367 (complementary to (converted) bottom strand) CT/GA/GA: 8567227 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 1203987823 Total methylated C's in CpG context: 16464158 Total methylated C's in CHG context: 1020445 Total methylated C's in CHH context: 4398768 Total methylated C's in Unknown context: 41528 Total unmethylated C's in CpG context: 137191904 Total unmethylated C's in CHG context: 209377026 Total unmethylated C's in CHH context: 835535522 Total unmethylated C's in Unknown context: 3013713 C methylated in CpG context: 10.7% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 1.4% Bismark completed in 0d 5h 22m 24s