Bismark report for: /gscratch/srlab/sr320/data/cg/zr3534_5_R1.fastp-trim.20201202.fq.gz and /gscratch/srlab/sr320/data/cg/zr3534_5_R2.fastp-trim.20201202.fq.gz (version: v0.21.0) Bismark was run with Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin/ with the specified options: -q --score-min L,0,-0.6 -p 8 --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: 84046138 Number of paired-end alignments with a unique best hit: 51585368 Mapping efficiency: 61.4% Sequence pairs with no alignments under any condition: 18797722 Sequence pairs did not map uniquely: 13663048 Sequence pairs which were discarded because genomic sequence could not be extracted: 101 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 12875770 ((converted) top strand) GA/CT/CT: 12866373 (complementary to (converted) top strand) GA/CT/GA: 12917286 (complementary to (converted) bottom strand) CT/GA/GA: 12925838 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 1796778652 Total methylated C's in CpG context: 26305118 Total methylated C's in CHG context: 1560817 Total methylated C's in CHH context: 6628303 Total methylated C's in Unknown context: 63678 Total unmethylated C's in CpG context: 207445585 Total unmethylated C's in CHG context: 312397279 Total unmethylated C's in CHH context: 1242441550 Total unmethylated C's in Unknown context: 4404111 C methylated in CpG context: 11.3% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 1.4% Bismark completed in 0d 7h 26m 18s