Bismark report for: /gscratch/srlab/sr320/data/olurida-bs/1_ATCACG_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: 9246318 Number of alignments with a unique best hit from the different alignments: 4354977 Mapping efficiency: 47.1% Sequences with no alignments under any condition: 137109 Sequences did not map uniquely: 4754232 Sequences which were discarded because genomic sequence could not be extracted: 3055 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 1705631 ((converted) top strand) CT/GA: 1704737 ((converted) bottom strand) GA/CT: 469284 (complementary to (converted) top strand) GA/GA: 472270 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 24632437 Total methylated C's in CpG context: 867950 Total methylated C's in CHG context: 113827 Total methylated C's in CHH context: 2657818 Total methylated C's in Unknown context: 46268 Total unmethylated C's in CpG context: 2076267 Total unmethylated C's in CHG context: 3866565 Total unmethylated C's in CHH context: 15050010 Total unmethylated C's in Unknown context: 80746 C methylated in CpG context: 29.5% C methylated in CHG context: 2.9% C methylated in CHH context: 15.0% C methylated in Unknown context (CN or CHN): 36.4% Bismark completed in 0d 0h 18m 17s