Bismark report for: /gscratch/scrubbed/samwhite/data/O_lurida/BSseq/whole_genome_BSseq_reads/20180830_trimgalore/4_TGACCA_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: 11560658 Number of alignments with a unique best hit from the different alignments: 5904119 Mapping efficiency: 51.1% Sequences with no alignments under any condition: 1722818 Sequences did not map uniquely: 3933721 Sequences which were discarded because genomic sequence could not be extracted: 4064 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 2832715 ((converted) top strand) CT/GA: 2833529 ((converted) bottom strand) GA/CT: 116844 (complementary to (converted) top strand) GA/GA: 116967 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 45555389 Total methylated C's in CpG context: 1816741 Total methylated C's in CHG context: 113208 Total methylated C's in CHH context: 1478548 Total methylated C's in Unknown context: 26295 Total unmethylated C's in CpG context: 4789205 Total unmethylated C's in CHG context: 8705545 Total unmethylated C's in CHH context: 28652142 Total unmethylated C's in Unknown context: 154700 C methylated in CpG context: 27.5% C methylated in CHG context: 1.3% C methylated in CHH context: 4.9% C methylated in Unknown context (CN or CHN): 14.5% Bismark completed in 0d 7h 5m 43s