Bismark report for: /home/sam/analyses/20180503_oly_methylseq_trimgalore/3_TTAGGC_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: 11555321 Number of alignments with a unique best hit from the different alignments: 4558848 Mapping efficiency: 39.5% Sequences with no alignments under any condition: 1568078 Sequences did not map uniquely: 5428395 Sequences which were discarded because genomic sequence could not be extracted: 8921 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 2082412 ((converted) top strand) CT/GA: 2076802 ((converted) bottom strand) GA/CT: 194744 (complementary to (converted) top strand) GA/GA: 195969 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 25864841 Total methylated C's in CpG context: 1008114 Total methylated C's in CHG context: 77277 Total methylated C's in CHH context: 1449502 Total methylated C's in Unknown context: 404 Total unmethylated C's in CpG context: 2566173 Total unmethylated C's in CHG context: 4698459 Total unmethylated C's in CHH context: 16065316 Total unmethylated C's in Unknown context: 4356 C methylated in CpG context: 28.2% C methylated in CHG context: 1.6% C methylated in CHH context: 8.3% C methylated in Unknown context (CN or CHN): 8.5% Bismark completed in 0d 10h 44m 9s