Bismark report for: /home/sam/analyses/20180503_oly_methylseq_trimgalore/6_GCCAAT_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: 12175584 Number of alignments with a unique best hit from the different alignments: 4744337 Mapping efficiency: 39.0% Sequences with no alignments under any condition: 1704908 Sequences did not map uniquely: 5726339 Sequences which were discarded because genomic sequence could not be extracted: 9628 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 2145577 ((converted) top strand) CT/GA: 2151177 ((converted) bottom strand) GA/CT: 218883 (complementary to (converted) top strand) GA/GA: 219072 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 26849935 Total methylated C's in CpG context: 1000055 Total methylated C's in CHG context: 99808 Total methylated C's in CHH context: 1612559 Total methylated C's in Unknown context: 422 Total unmethylated C's in CpG context: 2670919 Total unmethylated C's in CHG context: 4841111 Total unmethylated C's in CHH context: 16625483 Total unmethylated C's in Unknown context: 4711 C methylated in CpG context: 27.2% C methylated in CHG context: 2.0% C methylated in CHH context: 8.8% C methylated in Unknown context (CN or CHN): 8.2% Bismark completed in 0d 22h 31m 12s