Bismark report for: /gscratch/srlab/sr320/data/cg/zr3644_17_R1.fastp-trim.20201206.fq.gz and /gscratch/srlab/sr320/data/cg/zr3644_17_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,-0.2 -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: 57127374 Number of paired-end alignments with a unique best hit: 21998260 Mapping efficiency: 38.5% Sequence pairs with no alignments under any condition: 29217690 Sequence pairs did not map uniquely: 5911424 Sequence pairs which were discarded because genomic sequence could not be extracted: 949 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 5508925 ((converted) top strand) GA/CT/CT: 5478994 (complementary to (converted) top strand) GA/CT/GA: 5489780 (complementary to (converted) bottom strand) CT/GA/GA: 5519612 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 784014626 Total methylated C's in CpG context: 12262703 Total methylated C's in CHG context: 633324 Total methylated C's in CHH context: 2500503 Total methylated C's in Unknown context: 5428 Total unmethylated C's in CpG context: 90085935 Total unmethylated C's in CHG context: 139670160 Total unmethylated C's in CHH context: 538862001 Total unmethylated C's in Unknown context: 536395 C methylated in CpG context: 12.0% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 1.0% Bismark completed in 0d 7h 36m 32s