Bismark report for: /home/sam/analyses/20180503_oly_methylseq_trimgalore/zr1394_12_s456_trimmed.fq.gz (version: v0.19.1) 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 /home/sam/data/oly_methylseq/oly_genome/ with the specified options: -q --score-min L,0,-0.2 -p 16 --reorder --ignore-quals Final Alignment report ====================== Sequences analysed in total: 1000000 Number of alignments with a unique best hit from the different alignments: 358405 Mapping efficiency: 35.8% Sequences with no alignments under any condition: 249791 Sequences did not map uniquely: 391804 Sequences which were discarded because genomic sequence could not be extracted: 635 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 79135 ((converted) top strand) CT/GA: 78452 ((converted) bottom strand) GA/CT: 100583 (complementary to (converted) top strand) GA/GA: 99600 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2131173 Total methylated C's in CpG context: 249510 Total methylated C's in CHG context: 7748 Total methylated C's in CHH context: 104849 Total methylated C's in Unknown context: 63 Total unmethylated C's in CpG context: 60833 Total unmethylated C's in CHG context: 433479 Total unmethylated C's in CHH context: 1274754 Total unmethylated C's in Unknown context: 355 C methylated in CpG context: 80.4% C methylated in CHG context: 1.8% C methylated in CHH context: 7.6% C methylated in Unknown context (CN or CHN): 15.1% Bismark completed in 0d 3h 52m 5s