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/scrubbed/samwhite/data/O_lurida/BSseq/20180503_oly_genome_pbjelly_sjw_01_bismark/ 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: 6120182 Mapping efficiency: 52.9% Sequences with no alignments under any condition: 1415586 Sequences did not map uniquely: 4024890 Sequences which were discarded because genomic sequence could not be extracted: 15614 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 2943526 ((converted) top strand) CT/GA: 2944699 ((converted) bottom strand) GA/CT: 108115 (complementary to (converted) top strand) GA/GA: 108228 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 47056655 Total methylated C's in CpG context: 1889769 Total methylated C's in CHG context: 114764 Total methylated C's in CHH context: 1430716 Total methylated C's in Unknown context: 23580 Total unmethylated C's in CpG context: 4949099 Total unmethylated C's in CHG context: 9036311 Total unmethylated C's in CHH context: 29635996 Total unmethylated C's in Unknown context: 141728 C methylated in CpG context: 27.6% C methylated in CHG context: 1.3% C methylated in CHH context: 4.6% C methylated in Unknown context (CN or CHN): 14.3% Bismark completed in 0d 7h 22m 35s