Bismark report for: /home/sam/analyses/20180503_oly_methylseq_trimgalore/zr1394_17_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/20180503_oly_genome_pbjelly_sjw_01_bismark/ with the specified options: -q --score-min L,0,-0.2 -p 16 --reorder --ignore-quals Final Alignment report ====================== Sequences analysed in total: 42070546 Number of alignments with a unique best hit from the different alignments: 13402022 Mapping efficiency: 31.9% Sequences with no alignments under any condition: 11125453 Sequences did not map uniquely: 17543071 Sequences which were discarded because genomic sequence could not be extracted: 28967 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 3040693 ((converted) top strand) CT/GA: 3022357 ((converted) bottom strand) GA/CT: 3666380 (complementary to (converted) top strand) GA/GA: 3643625 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 83239424 Total methylated C's in CpG context: 13500223 Total methylated C's in CHG context: 381439 Total methylated C's in CHH context: 4279479 Total methylated C's in Unknown context: 2449 Total unmethylated C's in CpG context: 2090683 Total unmethylated C's in CHG context: 17571927 Total unmethylated C's in CHH context: 45415673 Total unmethylated C's in Unknown context: 16276 C methylated in CpG context: 86.6% C methylated in CHG context: 2.1% C methylated in CHH context: 8.6% C methylated in Unknown context (CN or CHN): 13.1% Bismark completed in 7d 14h 10m 52s