Bismark report for: /Volumes/web/nightingales/C_virginica/zr2096_5_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: 31778715 Number of alignments with a unique best hit from the different alignments: 19747789 Mapping efficiency: 62.1% Sequences with no alignments under any condition: 5004694 Sequences did not map uniquely: 7026232 Sequences which were discarded because genomic sequence could not be extracted: 17 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 4314666 ((converted) top strand) CT/GA: 4307837 ((converted) bottom strand) GA/CT: 5566381 (complementary to (converted) top strand) GA/GA: 5558888 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 329492591 Total methylated C's in CpG context: 27938657 Total methylated C's in CHG context: 2365484 Total methylated C's in CHH context: 9268835 Total methylated C's in Unknown context: 1295890 Total unmethylated C's in CpG context: 14160106 Total unmethylated C's in CHG context: 70486196 Total unmethylated C's in CHH context: 205273313 Total unmethylated C's in Unknown context: 5854414 C methylated in CpG context: 66.4% C methylated in CHG context: 3.2% C methylated in CHH context: 4.3% C methylated in Unknown context (CN or CHN): 18.1% Bismark completed in 1d 12h 54m 37s