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/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: 12409649 Number of alignments with a unique best hit from the different alignments: 6451725 Mapping efficiency: 52.0% Sequences with no alignments under any condition: 1647581 Sequences did not map uniquely: 4310343 Sequences which were discarded because genomic sequence could not be extracted: 16975 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 3070334 ((converted) top strand) CT/GA: 3081903 ((converted) bottom strand) GA/CT: 143812 (complementary to (converted) top strand) GA/GA: 138701 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 49744541 Total methylated C's in CpG context: 1895479 Total methylated C's in CHG context: 178428 Total methylated C's in CHH context: 1839322 Total methylated C's in Unknown context: 28097 Total unmethylated C's in CpG context: 5436344 Total unmethylated C's in CHG context: 9548299 Total unmethylated C's in CHH context: 30846669 Total unmethylated C's in Unknown context: 154404 C methylated in CpG context: 25.9% C methylated in CHG context: 1.8% C methylated in CHH context: 5.6% C methylated in Unknown context (CN or CHN): 15.4% Bismark completed in 0d 11h 28m 52s