Bismark report for: /home/sam/analyses/20180503_oly_methylseq_trimgalore/zr1394_16_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: 306879 Mapping efficiency: 30.7% Sequences with no alignments under any condition: 260121 Sequences did not map uniquely: 433000 Sequences which were discarded because genomic sequence could not be extracted: 747 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 69176 ((converted) top strand) CT/GA: 68695 ((converted) bottom strand) GA/CT: 84270 (complementary to (converted) top strand) GA/GA: 83991 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 1920575 Total methylated C's in CpG context: 321346 Total methylated C's in CHG context: 8408 Total methylated C's in CHH context: 91489 Total methylated C's in Unknown context: 66 Total unmethylated C's in CpG context: 52800 Total unmethylated C's in CHG context: 380224 Total unmethylated C's in CHH context: 1066308 Total unmethylated C's in Unknown context: 353 C methylated in CpG context: 85.9% C methylated in CHG context: 2.2% C methylated in CHH context: 7.9% C methylated in Unknown context (CN or CHN): 15.8% Bismark completed in 0d 5h 7m 47s