Bismark report for: /gscratch/scrubbed/samwhite/data/O_lurida/BSseq/whole_genome_BSseq_reads/20180830_trimgalore/7_CAGATC_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,-0.2 -p 28 --reorder --ignore-quals Final Alignment report ====================== Sequences analysed in total: 10253191 Number of alignments with a unique best hit from the different alignments: 4435070 Mapping efficiency: 43.3% Sequences with no alignments under any condition: 2594667 Sequences did not map uniquely: 3223454 Sequences which were discarded because genomic sequence could not be extracted: 8355 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 2187545 ((converted) top strand) CT/GA: 2184804 ((converted) bottom strand) GA/CT: 27236 (complementary to (converted) top strand) GA/GA: 27130 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 34295566 Total methylated C's in CpG context: 1401145 Total methylated C's in CHG context: 63667 Total methylated C's in CHH context: 555550 Total methylated C's in Unknown context: 1202 Total unmethylated C's in CpG context: 3661318 Total unmethylated C's in CHG context: 6758906 Total unmethylated C's in CHH context: 21854980 Total unmethylated C's in Unknown context: 27615 C methylated in CpG context: 27.7% C methylated in CHG context: 0.9% C methylated in CHH context: 2.5% C methylated in Unknown context (CN or CHN): 4.2% Bismark completed in 0d 10h 47m 40s