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/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: 87834637 Number of alignments with a unique best hit from the different alignments: 26569183 Mapping efficiency: 30.2% Sequences with no alignments under any condition: 24154445 Sequences did not map uniquely: 37111009 Sequences which were discarded because genomic sequence could not be extracted: 56676 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 5941705 ((converted) top strand) CT/GA: 5922312 ((converted) bottom strand) GA/CT: 7346624 (complementary to (converted) top strand) GA/GA: 7301866 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 164461697 Total methylated C's in CpG context: 25351189 Total methylated C's in CHG context: 698721 Total methylated C's in CHH context: 7834266 Total methylated C's in Unknown context: 4829 Total unmethylated C's in CpG context: 4293547 Total unmethylated C's in CHG context: 31618187 Total unmethylated C's in CHH context: 94665787 Total unmethylated C's in Unknown context: 32870 C methylated in CpG context: 85.5% C methylated in CHG context: 2.2% C methylated in CHH context: 7.6% C methylated in Unknown context (CN or CHN): 12.8% Bismark completed in 5d 9h 52m 53s