Bismark report for: /gscratch/srlab/sr320/data/cg/zr3644_18_R1.fastp-trim.20201206.fq.gz and /gscratch/srlab/sr320/data/cg/zr3644_18_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: 50675924 Number of paired-end alignments with a unique best hit: 19762420 Mapping efficiency: 39.0% Sequence pairs with no alignments under any condition: 26011820 Sequence pairs did not map uniquely: 4901684 Sequence pairs which were discarded because genomic sequence could not be extracted: 854 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 4968187 ((converted) top strand) GA/CT/CT: 4901333 (complementary to (converted) top strand) GA/CT/GA: 4914664 (complementary to (converted) bottom strand) CT/GA/GA: 4977382 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 702187735 Total methylated C's in CpG context: 11122944 Total methylated C's in CHG context: 563351 Total methylated C's in CHH context: 2209287 Total methylated C's in Unknown context: 4640 Total unmethylated C's in CpG context: 79862407 Total unmethylated C's in CHG context: 125026145 Total unmethylated C's in CHH context: 483403601 Total unmethylated C's in Unknown context: 474810 C methylated in CpG context: 12.2% C methylated in CHG context: 0.4% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 1.0% Bismark completed in 0d 2h 32m 10s