Bismark report for: /gscratch/srlab/sr320/data/cg/zr3644_12_R1.fastp-trim.20201206.fq.gz and /gscratch/srlab/sr320/data/cg/zr3644_12_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: 46634543 Number of paired-end alignments with a unique best hit: 29003146 Mapping efficiency: 62.2% Sequence pairs with no alignments under any condition: 11943464 Sequence pairs did not map uniquely: 5687933 Sequence pairs which were discarded because genomic sequence could not be extracted: 3106 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 7225443 ((converted) top strand) GA/CT/CT: 7291497 (complementary to (converted) top strand) GA/CT/GA: 7268237 (complementary to (converted) bottom strand) CT/GA/GA: 7214863 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 1012845722 Total methylated C's in CpG context: 12471833 Total methylated C's in CHG context: 803989 Total methylated C's in CHH context: 3447972 Total methylated C's in Unknown context: 31058 Total unmethylated C's in CpG context: 113531079 Total unmethylated C's in CHG context: 170581064 Total unmethylated C's in CHH context: 712009785 Total unmethylated C's in Unknown context: 2618222 C methylated in CpG context: 9.9% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 1.2% Bismark completed in 0d 4h 34m 7s