Bismark report for: /Volumes/web/nightingales/C_virginica/zr2096_4_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: 24341968 Number of alignments with a unique best hit from the different alignments: 15265144 Mapping efficiency: 62.7% Sequences with no alignments under any condition: 3520904 Sequences did not map uniquely: 5555920 Sequences which were discarded because genomic sequence could not be extracted: 10 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 3730487 ((converted) top strand) CT/GA: 3752378 ((converted) bottom strand) GA/CT: 3887365 (complementary to (converted) top strand) GA/GA: 3894904 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 245031474 Total methylated C's in CpG context: 20763140 Total methylated C's in CHG context: 1771156 Total methylated C's in CHH context: 7112911 Total methylated C's in Unknown context: 943782 Total unmethylated C's in CpG context: 11273670 Total unmethylated C's in CHG context: 53802370 Total unmethylated C's in CHH context: 150308227 Total unmethylated C's in Unknown context: 4255730 C methylated in CpG context: 64.8% C methylated in CHG context: 3.2% C methylated in CHH context: 4.5% C methylated in Unknown context (CN or CHN): 18.2% Bismark completed in 1d 2h 27m 48s