Bismark report for: /home/sam/analyses/20180503_oly_methylseq_trimgalore/8_ACTTGA_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: 13949213 Number of alignments with a unique best hit from the different alignments: 5449339 Mapping efficiency: 39.1% Sequences with no alignments under any condition: 1876942 Sequences did not map uniquely: 6622932 Sequences which were discarded because genomic sequence could not be extracted: 11076 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 2485153 ((converted) top strand) CT/GA: 2481240 ((converted) bottom strand) GA/CT: 235658 (complementary to (converted) top strand) GA/GA: 236212 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 30870373 Total methylated C's in CpG context: 1093598 Total methylated C's in CHG context: 91495 Total methylated C's in CHH context: 1695039 Total methylated C's in Unknown context: 496 Total unmethylated C's in CpG context: 3116289 Total unmethylated C's in CHG context: 5620981 Total unmethylated C's in CHH context: 19252971 Total unmethylated C's in Unknown context: 5381 C methylated in CpG context: 26.0% C methylated in CHG context: 1.6% C methylated in CHH context: 8.1% C methylated in Unknown context (CN or CHN): 8.4% Bismark completed in 1d 6h 26m 9s