Bismark report for: /home/sam/analyses/20180503_oly_methylseq_trimgalore/1_ATCACG_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: 9246318 Number of alignments with a unique best hit from the different alignments: 3669950 Mapping efficiency: 39.7% Sequences with no alignments under any condition: 1217825 Sequences did not map uniquely: 4358543 Sequences which were discarded because genomic sequence could not be extracted: 7392 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 1676051 ((converted) top strand) CT/GA: 1675797 ((converted) bottom strand) GA/CT: 154629 (complementary to (converted) top strand) GA/GA: 156081 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 20736625 Total methylated C's in CpG context: 818911 Total methylated C's in CHG context: 63887 Total methylated C's in CHH context: 1148031 Total methylated C's in Unknown context: 337 Total unmethylated C's in CpG context: 2004289 Total unmethylated C's in CHG context: 3770713 Total unmethylated C's in CHH context: 12930794 Total unmethylated C's in Unknown context: 3562 C methylated in CpG context: 29.0% C methylated in CHG context: 1.7% C methylated in CHH context: 8.2% C methylated in Unknown context (CN or CHN): 8.6% Bismark completed in 0d 3h 5m 19s