Bismark report for: /gscratch/srlab/sr320/data/olurida-bs/6_GCCAAT_L001_R1_001_trimmed.fq.gz (version: v0.22.3) Option '--non_directional' specified: alignments to all strands were being performed (OT, OB, CTOT, CTOB) Bismark was run with Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/olurida-bs/genome/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals Final Alignment report ====================== Sequences analysed in total: 12175584 Number of alignments with a unique best hit from the different alignments: 5696470 Mapping efficiency: 46.8% Sequences with no alignments under any condition: 199356 Sequences did not map uniquely: 6279758 Sequences which were discarded because genomic sequence could not be extracted: 3830 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 2189758 ((converted) top strand) CT/GA: 2194577 ((converted) bottom strand) GA/CT: 653682 (complementary to (converted) top strand) GA/GA: 654623 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 32257871 Total methylated C's in CpG context: 1064240 Total methylated C's in CHG context: 167997 Total methylated C's in CHH context: 3734153 Total methylated C's in Unknown context: 65346 Total unmethylated C's in CpG context: 2785236 Total unmethylated C's in CHG context: 4981668 Total unmethylated C's in CHH context: 19524577 Total unmethylated C's in Unknown context: 109623 C methylated in CpG context: 27.6% C methylated in CHG context: 3.3% C methylated in CHH context: 16.1% C methylated in Unknown context (CN or CHN): 37.3% Bismark completed in 0d 0h 24m 8s