Bismark report for: /Volumes/web/nightingales/C_virginica/zr2096_8_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: 10000 Number of alignments with a unique best hit from the different alignments: 5645 Mapping efficiency: 56.5% Sequences with no alignments under any condition: 2318 Sequences did not map uniquely: 2037 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: 1260 ((converted) top strand) CT/GA: 1253 ((converted) bottom strand) GA/CT: 1552 (complementary to (converted) top strand) GA/GA: 1580 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 92445 Total methylated C's in CpG context: 7495 Total methylated C's in CHG context: 721 Total methylated C's in CHH context: 2989 Total methylated C's in Unknown context: 372 Total unmethylated C's in CpG context: 3847 Total unmethylated C's in CHG context: 19920 Total unmethylated C's in CHH context: 57473 Total unmethylated C's in Unknown context: 1544 C methylated in CpG context: 66.1% C methylated in CHG context: 3.5% C methylated in CHH context: 4.9% C methylated in Unknown context (CN or CHN): 19.4% Bismark completed in 0d 0h 3m 29s