Bismark report for: /gscratch/srlab/sr320/data/olurida-bs/combined.fq.gz (version: v0.22.3) Option '--directional' specified (default mode): alignments to complementary strands (CTOT, CTOB) were ignored (i.e. not performed) 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: 92334932 Number of alignments with a unique best hit from the different alignments: 40417426 Mapping efficiency: 43.8% Sequences with no alignments under any condition: 11929375 Sequences did not map uniquely: 39988131 Sequences which were discarded because genomic sequence could not be extracted: 37499 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 20219240 ((converted) top strand) CT/GA: 20160687 ((converted) bottom strand) GA/CT: 0 (complementary to (converted) top strand) GA/GA: 0 (complementary to (converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 217529869 Total methylated C's in CpG context: 8289193 Total methylated C's in CHG context: 521677 Total methylated C's in CHH context: 2297463 Total methylated C's in Unknown context: 31624 Total unmethylated C's in CpG context: 24139397 Total unmethylated C's in CHG context: 42918302 Total unmethylated C's in CHH context: 139363837 Total unmethylated C's in Unknown context: 541613 C methylated in CpG context: 25.6% C methylated in CHG context: 1.2% C methylated in CHH context: 1.6% C methylated in Unknown context (CN or CHN): 5.5% Bismark completed in 0d 2h 12m 33s