Bismark report for: /gscratch/scrubbed/samwhite/data/O_lurida/BSseq/whole_genome_BSseq_reads/20180830_trimgalore/1_ATCACG_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: 9365330 Number of alignments with a unique best hit from the different alignments: 4066105 Mapping efficiency: 43.4% Sequences with no alignments under any condition: 2378548 Sequences did not map uniquely: 2920677 Sequences which were discarded because genomic sequence could not be extracted: 7494 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 2002168 ((converted) top strand) CT/GA: 1999822 ((converted) bottom strand) GA/CT: 27767 (complementary to (converted) top strand) GA/GA: 28854 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 31606927 Total methylated C's in CpG context: 1332201 Total methylated C's in CHG context: 73999 Total methylated C's in CHH context: 573400 Total methylated C's in Unknown context: 1354 Total unmethylated C's in CpG context: 3374891 Total unmethylated C's in CHG context: 6217392 Total unmethylated C's in CHH context: 20035044 Total unmethylated C's in Unknown context: 27054 C methylated in CpG context: 28.3% C methylated in CHG context: 1.2% C methylated in CHH context: 2.8% C methylated in Unknown context (CN or CHN): 4.8% Bismark completed in 0d 1h 16m 30s