Bismark report for: zr2096_7_s1_R1_val_1.fq.gz and zr2096_7_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: 518103 Mapping efficiency: 51.8% Sequence pairs with no alignments under any condition: 286502 Sequence pairs did not map uniquely: 195395 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: 131416 ((converted) top strand) GA/CT/CT: 127670 (complementary to (converted) top strand) GA/CT/GA: 127990 (complementary to (converted) bottom strand) CT/GA/GA: 131027 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 13806945 Total methylated C's in CpG context: 1263772 Total methylated C's in CHG context: 78374 Total methylated C's in CHH context: 384212 Total methylated C's in Unknown context: 36797 Total unmethylated C's in CpG context: 483667 Total unmethylated C's in CHG context: 2916755 Total unmethylated C's in CHH context: 8680165 Total unmethylated C's in Unknown context: 171742 C methylated in CpG context: 72.3% C methylated in CHG context: 2.6% C methylated in CHH context: 4.2% C methylated in unknown context (CN or CHN): 17.6% Bismark completed in 0d 0h 10m 2s