Bismark report for: /Volumes/web/nightingales/C_virginica/zr2096_6_s1_R2.fastq.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 /Users/yaamini/Documents/project-virginica-oa/analyses/2018-04-27-Bismark/2018-04-27-Bismark-Inputs/ with the specified options: -q --score-min L,0,-1.2 --ignore-quals Final Alignment report ====================== Sequences analysed in total: 24237290 Number of alignments with a unique best hit from the different alignments: 15417762 Mapping efficiency: 63.6% Sequences with no alignments under any condition: 3104041 Sequences did not map uniquely: 5715487 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 3397789 ((converted) top strand) CT/GA: 3409067 ((converted) bottom strand) GA/CT: 4301287 (complementary to (converted) top strand) GA/GA: 4309619 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 250995696 Total methylated C's in CpG context: 23783200 Total methylated C's in CHG context: 1785409 Total methylated C's in CHH context: 7007182 Total methylated C's in Unknown context: 956844 Total unmethylated C's in CpG context: 9457782 Total unmethylated C's in CHG context: 54931812 Total unmethylated C's in CHH context: 154030311 Total unmethylated C's in Unknown context: 4451239 C methylated in CpG context: 71.5% C methylated in CHG context: 3.1% C methylated in CHH context: 4.4% C methylated in Unknown context (CN or CHN): 17.7% Bismark completed in 1d 18h 27m 27s