Bismark report for: /gscratch/srlab/sr320/data/olurida-bs/8_ACTTGA_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: 13949213 Number of alignments with a unique best hit from the different alignments: 6487669 Mapping efficiency: 46.5% Sequences with no alignments under any condition: 214634 Sequences did not map uniquely: 7246910 Sequences which were discarded because genomic sequence could not be extracted: 4632 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 2531677 ((converted) top strand) CT/GA: 2525255 ((converted) bottom strand) GA/CT: 712380 (complementary to (converted) top strand) GA/GA: 713725 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 36776252 Total methylated C's in CpG context: 1160722 Total methylated C's in CHG context: 164820 Total methylated C's in CHH context: 3984847 Total methylated C's in Unknown context: 69576 Total unmethylated C's in CpG context: 3227776 Total unmethylated C's in CHG context: 5765497 Total unmethylated C's in CHH context: 22472590 Total unmethylated C's in Unknown context: 122119 C methylated in CpG context: 26.4% C methylated in CHG context: 2.8% C methylated in CHH context: 15.1% C methylated in Unknown context (CN or CHN): 36.3% Bismark completed in 0d 0h 27m 21s