Bismark report for: /gscratch/srlab/sr320/data/cg/zr3644_1_R1.fastp-trim.20201206.fq.gz and /gscratch/srlab/sr320/data/cg/zr3644_1_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: 50613363 Number of paired-end alignments with a unique best hit: 19323467 Mapping efficiency: 38.2% Sequence pairs with no alignments under any condition: 26287539 Sequence pairs did not map uniquely: 5002357 Sequence pairs which were discarded because genomic sequence could not be extracted: 913 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 4886650 ((converted) top strand) GA/CT/CT: 4769500 (complementary to (converted) top strand) GA/CT/GA: 4774029 (complementary to (converted) bottom strand) CT/GA/GA: 4892375 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 683354629 Total methylated C's in CpG context: 9784856 Total methylated C's in CHG context: 517067 Total methylated C's in CHH context: 2042367 Total methylated C's in Unknown context: 4191 Total unmethylated C's in CpG context: 78329567 Total unmethylated C's in CHG context: 121315756 Total unmethylated C's in CHH context: 471365016 Total unmethylated C's in Unknown context: 459827 C methylated in CpG context: 11.1% C methylated in CHG context: 0.4% C methylated in CHH context: 0.4% C methylated in unknown context (CN or CHN): 0.9% Bismark completed in 0d 2h 28m 38s