Bismark report for: /Volumes/web/nightingales/C_virginica/zr2096_8_s1_R1.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: 29761837 Number of alignments with a unique best hit from the different alignments: 16990385 Mapping efficiency: 57.1% Sequences with no alignments under any condition: 6827921 Sequences did not map uniquely: 5943531 Sequences which were discarded because genomic sequence could not be extracted: 45 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 4025767 ((converted) top strand) CT/GA: 4021055 ((converted) bottom strand) GA/CT: 4484664 (complementary to (converted) top strand) GA/GA: 4458854 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 278494729 Total methylated C's in CpG context: 22323794 Total methylated C's in CHG context: 2129240 Total methylated C's in CHH context: 8817866 Total methylated C's in Unknown context: 1167252 Total unmethylated C's in CpG context: 11895762 Total unmethylated C's in CHG context: 60259984 Total unmethylated C's in CHH context: 173068083 Total unmethylated C's in Unknown context: 4927629 C methylated in CpG context: 65.2% C methylated in CHG context: 3.4% C methylated in CHH context: 4.8% C methylated in Unknown context (CN or CHN): 19.2% Bismark completed in 0d 3h 34m 3s