Bismark report for: /Volumes/web/nightingales/C_virginica/zr2096_3_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: 29892002 Number of alignments with a unique best hit from the different alignments: 18915974 Mapping efficiency: 63.3% Sequences with no alignments under any condition: 3541197 Sequences did not map uniquely: 7434831 Sequences which were discarded because genomic sequence could not be extracted: 3 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 4443901 ((converted) top strand) CT/GA: 4467756 ((converted) bottom strand) GA/CT: 4998705 (complementary to (converted) top strand) GA/GA: 5005609 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 328453836 Total methylated C's in CpG context: 36071858 Total methylated C's in CHG context: 2415432 Total methylated C's in CHH context: 8353242 Total methylated C's in Unknown context: 1241841 Total unmethylated C's in CpG context: 11743681 Total unmethylated C's in CHG context: 73244050 Total unmethylated C's in CHH context: 196625573 Total unmethylated C's in Unknown context: 5501487 C methylated in CpG context: 75.4% C methylated in CHG context: 3.2% C methylated in CHH context: 4.1% C methylated in Unknown context (CN or CHN): 18.4% Bismark completed in 0d 20h 28m 53s