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/oly_genome/ with the specified options: -q --score-min L,0,-0.2 -p 16 --reorder --ignore-quals Final Alignment report ====================== Sequences analysed in total: 1000000 Number of alignments with a unique best hit from the different alignments: 395712 Mapping efficiency: 39.6% Sequences with no alignments under any condition: 129226 Sequences did not map uniquely: 475062 Sequences which were discarded because genomic sequence could not be extracted: 838 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 179691 ((converted) top strand) CT/GA: 180213 ((converted) bottom strand) GA/CT: 17490 (complementary to (converted) top strand) GA/GA: 17480 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2235158 Total methylated C's in CpG context: 82834 Total methylated C's in CHG context: 7846 Total methylated C's in CHH context: 129683 Total methylated C's in Unknown context: 39 Total unmethylated C's in CpG context: 223364 Total unmethylated C's in CHG context: 403520 Total unmethylated C's in CHH context: 1387911 Total unmethylated C's in Unknown context: 383 C methylated in CpG context: 27.1% C methylated in CHG context: 1.9% C methylated in CHH context: 8.5% C methylated in Unknown context (CN or CHN): 9.2% Bismark completed in 0d 2h 10m 41s