Bismark report for: /gscratch/srlab/sr320/data/olurida-bs/7_CAGATC_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: 10113854 Number of alignments with a unique best hit from the different alignments: 4732904 Mapping efficiency: 46.8% Sequences with no alignments under any condition: 144592 Sequences did not map uniquely: 5236358 Sequences which were discarded because genomic sequence could not be extracted: 3226 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 1852528 ((converted) top strand) CT/GA: 1848121 ((converted) bottom strand) GA/CT: 513555 (complementary to (converted) top strand) GA/GA: 515474 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 26664014 Total methylated C's in CpG context: 903842 Total methylated C's in CHG context: 107795 Total methylated C's in CHH context: 2867247 Total methylated C's in Unknown context: 50394 Total unmethylated C's in CpG context: 2225682 Total unmethylated C's in CHG context: 4168082 Total unmethylated C's in CHH context: 16391366 Total unmethylated C's in Unknown context: 86742 C methylated in CpG context: 28.9% C methylated in CHG context: 2.5% C methylated in CHH context: 14.9% C methylated in Unknown context (CN or CHN): 36.7% Bismark completed in 0d 0h 20m 4s