Bismark report for: /home/sam/analyses/20180503_oly_methylseq_trimgalore/zr1394_14_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: 308475 Mapping efficiency: 30.8% Sequences with no alignments under any condition: 260477 Sequences did not map uniquely: 431048 Sequences which were discarded because genomic sequence could not be extracted: 686 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 68300 ((converted) top strand) CT/GA: 67907 ((converted) bottom strand) GA/CT: 86057 (complementary to (converted) top strand) GA/GA: 85525 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 1909368 Total methylated C's in CpG context: 297129 Total methylated C's in CHG context: 7858 Total methylated C's in CHH context: 86763 Total methylated C's in Unknown context: 54 Total unmethylated C's in CpG context: 50101 Total unmethylated C's in CHG context: 370495 Total unmethylated C's in CHH context: 1097022 Total unmethylated C's in Unknown context: 378 C methylated in CpG context: 85.6% C methylated in CHG context: 2.1% C methylated in CHH context: 7.3% C methylated in Unknown context (CN or CHN): 12.5% Bismark completed in 0d 4h 30m 8s