Bismark report for: /gscratch/scrubbed/samwhite/data/O_lurida/BSseq/whole_genome_BSseq_reads/20180830_trimgalore/6_GCCAAT_L001_R1_001_trimmed.fq.gz (version: v0.19.0) 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 /gscratch/srlab/sam/data/O_lurida/oly_genome_assemblies/Olurida_v081/oly_v081_bismark_genome/ with the specified options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals Final Alignment report ====================== Sequences analysed in total: 12409649 Number of alignments with a unique best hit from the different alignments: 6223300 Mapping efficiency: 50.1% Sequences with no alignments under any condition: 1972814 Sequences did not map uniquely: 4213535 Sequences which were discarded because genomic sequence could not be extracted: 4621 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 2953153 ((converted) top strand) CT/GA: 2964910 ((converted) bottom strand) GA/CT: 152444 (complementary to (converted) top strand) GA/GA: 148172 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 48160123 Total methylated C's in CpG context: 1821503 Total methylated C's in CHG context: 174253 Total methylated C's in CHH context: 1882872 Total methylated C's in Unknown context: 31051 Total unmethylated C's in CpG context: 5263336 Total unmethylated C's in CHG context: 9194875 Total unmethylated C's in CHH context: 29823284 Total unmethylated C's in Unknown context: 168165 C methylated in CpG context: 25.7% C methylated in CHG context: 1.9% C methylated in CHH context: 5.9% C methylated in Unknown context (CN or CHN): 15.6% Bismark completed in 0d 11h 2m 44s