Bismark report for: /gscratch/srlab/sr320/data/olurida-bs/5_ACAGTG_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: 12231319 Number of alignments with a unique best hit from the different alignments: 5718874 Mapping efficiency: 46.8% Sequences with no alignments under any condition: 184967 Sequences did not map uniquely: 6327478 Sequences which were discarded because genomic sequence could not be extracted: 3958 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 2232041 ((converted) top strand) CT/GA: 2230452 ((converted) bottom strand) GA/CT: 625277 (complementary to (converted) top strand) GA/GA: 627146 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 32455254 Total methylated C's in CpG context: 1107493 Total methylated C's in CHG context: 149103 Total methylated C's in CHH context: 3559852 Total methylated C's in Unknown context: 62167 Total unmethylated C's in CpG context: 2805384 Total unmethylated C's in CHG context: 5099491 Total unmethylated C's in CHH context: 19733931 Total unmethylated C's in Unknown context: 107662 C methylated in CpG context: 28.3% C methylated in CHG context: 2.8% C methylated in CHH context: 15.3% C methylated in Unknown context (CN or CHN): 36.6% Bismark completed in 0d 0h 24m 8s