Bismark report for: /gscratch/scrubbed/samwhite/data/O_lurida/BSseq/whole_genome_BSseq_reads/20180830_trimgalore/3_TTAGGC_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: 11758842 Number of alignments with a unique best hit from the different alignments: 6206512 Mapping efficiency: 52.8% Sequences with no alignments under any condition: 1478224 Sequences did not map uniquely: 4074106 Sequences which were discarded because genomic sequence could not be extracted: 15657 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 2980075 ((converted) top strand) CT/GA: 2978037 ((converted) bottom strand) GA/CT: 115504 (complementary to (converted) top strand) GA/GA: 117239 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 48057963 Total methylated C's in CpG context: 1896372 Total methylated C's in CHG context: 135635 Total methylated C's in CHH context: 1558137 Total methylated C's in Unknown context: 26480 Total unmethylated C's in CpG context: 5264793 Total unmethylated C's in CHG context: 9257683 Total unmethylated C's in CHH context: 29945343 Total unmethylated C's in Unknown context: 154704 C methylated in CpG context: 26.5% C methylated in CHG context: 1.4% C methylated in CHH context: 4.9% C methylated in Unknown context (CN or CHN): 14.6% Bismark completed in 0d 5h 27m 34s