Bismark report for: /home/sam/analyses/20180503_oly_methylseq_trimgalore/2_CGATGT_L001_R1_001_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: 11654467 Number of alignments with a unique best hit from the different alignments: 4581756 Mapping efficiency: 39.3% Sequences with no alignments under any condition: 1541276 Sequences did not map uniquely: 5531435 Sequences which were discarded because genomic sequence could not be extracted: 9178 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 2080629 ((converted) top strand) CT/GA: 2075553 ((converted) bottom strand) GA/CT: 208122 (complementary to (converted) top strand) GA/GA: 208274 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 25938456 Total methylated C's in CpG context: 995559 Total methylated C's in CHG context: 112417 Total methylated C's in CHH context: 1550012 Total methylated C's in Unknown context: 422 Total unmethylated C's in CpG context: 2519867 Total unmethylated C's in CHG context: 4659852 Total unmethylated C's in CHH context: 16100749 Total unmethylated C's in Unknown context: 4277 C methylated in CpG context: 28.3% C methylated in CHG context: 2.4% C methylated in CHH context: 8.8% C methylated in Unknown context (CN or CHN): 9.0% Bismark completed in 0d 6h 56m 19s