Bismark report for: /gscratch/srlab/sr320/data/olurida-bs/4_TGACCA_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: 11408856 Number of alignments with a unique best hit from the different alignments: 5364918 Mapping efficiency: 47.0% Sequences with no alignments under any condition: 163003 Sequences did not map uniquely: 5880935 Sequences which were discarded because genomic sequence could not be extracted: 3728 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 2109625 ((converted) top strand) CT/GA: 2109791 ((converted) bottom strand) GA/CT: 570642 (complementary to (converted) top strand) GA/GA: 571132 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 30242630 Total methylated C's in CpG context: 1073001 Total methylated C's in CHG context: 126723 Total methylated C's in CHH context: 3190332 Total methylated C's in Unknown context: 55634 Total unmethylated C's in CpG context: 2530272 Total unmethylated C's in CHG context: 4740036 Total unmethylated C's in CHH context: 18582266 Total unmethylated C's in Unknown context: 99087 C methylated in CpG context: 29.8% C methylated in CHG context: 2.6% C methylated in CHH context: 14.7% C methylated in Unknown context (CN or CHN): 36.0% Bismark completed in 0d 0h 22m 44s