Bismark report for: /gscratch/srlab/sr320/data/cg/zr3644_6_R1.fastp-trim.20201206.fq.gz and /gscratch/srlab/sr320/data/cg/zr3644_6_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: 52883485 Number of paired-end alignments with a unique best hit: 32927367 Mapping efficiency: 62.3% Sequence pairs with no alignments under any condition: 13405823 Sequence pairs did not map uniquely: 6550295 Sequence pairs which were discarded because genomic sequence could not be extracted: 3803 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 8241768 ((converted) top strand) GA/CT/CT: 8228543 (complementary to (converted) top strand) GA/CT/GA: 8222799 (complementary to (converted) bottom strand) CT/GA/GA: 8230454 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 1161276812 Total methylated C's in CpG context: 15428548 Total methylated C's in CHG context: 983123 Total methylated C's in CHH context: 4234417 Total methylated C's in Unknown context: 37887 Total unmethylated C's in CpG context: 131035907 Total unmethylated C's in CHG context: 200625235 Total unmethylated C's in CHH context: 808969582 Total unmethylated C's in Unknown context: 2915905 C methylated in CpG context: 10.5% 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 5h 8m 54s