Bismark report for: zr2096_8_s1_R1_val_1.fq.gz and zr2096_8_s1_R2_val_2.fq.gz (version: v0.19.0) Bismark was run with Bowtie 2 against the bisulfite genome of /Volumes/Serine/wd/18-03-15/genome/ with the specified options: -q --score-min L,0,-1.2 -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: 1000000 Number of paired-end alignments with a unique best hit: 481891 Mapping efficiency: 48.2% Sequence pairs with no alignments under any condition: 337604 Sequence pairs did not map uniquely: 180505 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: 122028 ((converted) top strand) GA/CT/CT: 119189 (complementary to (converted) top strand) GA/CT/GA: 118638 (complementary to (converted) bottom strand) CT/GA/GA: 122036 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 12325890 Total methylated C's in CpG context: 992024 Total methylated C's in CHG context: 72967 Total methylated C's in CHH context: 451622 Total methylated C's in Unknown context: 42077 Total unmethylated C's in CpG context: 486713 Total unmethylated C's in CHG context: 2574344 Total unmethylated C's in CHH context: 7748220 Total unmethylated C's in Unknown context: 161022 C methylated in CpG context: 67.1% C methylated in CHG context: 2.8% C methylated in CHH context: 5.5% C methylated in unknown context (CN or CHN): 20.7% Bismark completed in 0d 0h 9m 20s