Bismark report for: /gscratch/srlab/sr320/data/olurida-bs/1_ATCACG_L001_R1_001_trimmed.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: 9246318 Number of alignments with a unique best hit from the different alignments: 4067513 Mapping efficiency: 44.0% Sequences with no alignments under any condition: 1179217 Sequences did not map uniquely: 3999588 Sequences which were discarded because genomic sequence could not be extracted: 3816 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 2034763 ((converted) top strand) CT/GA: 2028934 ((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: 21885255 Total methylated C's in CpG context: 866566 Total methylated C's in CHG context: 50314 Total methylated C's in CHH context: 214171 Total methylated C's in Unknown context: 3116 Total unmethylated C's in CpG context: 2383138 Total unmethylated C's in CHG context: 4326724 Total unmethylated C's in CHH context: 14044342 Total unmethylated C's in Unknown context: 53884 C methylated in CpG context: 26.7% C methylated in CHG context: 1.1% C methylated in CHH context: 1.5% C methylated in Unknown context (CN or CHN): 5.5% Bismark completed in 0d 0h 13m 45s