Bismark report for: /gscratch/srlab/sr320/data/cg-big/zr3534_2_R1.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3534_2_R2.fastp.fq.gz (version: v0.22.3) Bismark was run with Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ 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: 100000 Number of paired-end alignments with a unique best hit: 61056 Mapping efficiency: 61.1% Sequence pairs with no alignments under any condition: 22398 Sequence pairs did not map uniquely: 16546 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 15479 ((converted) top strand) GA/CT/CT: 15217 (complementary to (converted) top strand) GA/CT/GA: 15036 (complementary to (converted) bottom strand) CT/GA/GA: 15324 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2137198 Total methylated C's in CpG context: 28100 Total methylated C's in CHG context: 1748 Total methylated C's in CHH context: 7871 Total methylated C's in Unknown context: 52 Total unmethylated C's in CpG context: 252518 Total unmethylated C's in CHG context: 373045 Total unmethylated C's in CHH context: 1473916 Total unmethylated C's in Unknown context: 5087 C methylated in CpG context: 10.0% 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 0h 0m 49s