Bismark report for: /Volumes/web/nightingales/C_virginica/zr2096_9_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: 32636231 Number of alignments with a unique best hit from the different alignments: 20265490 Mapping efficiency: 62.1% Sequences with no alignments under any condition: 4888304 Sequences did not map uniquely: 7482437 Sequences which were discarded because genomic sequence could not be extracted: 11 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 5049016 ((converted) top strand) CT/GA: 5071393 ((converted) bottom strand) GA/CT: 5069175 (complementary to (converted) top strand) GA/GA: 5075895 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 358117909 Total methylated C's in CpG context: 37990898 Total methylated C's in CHG context: 2989094 Total methylated C's in CHH context: 10058613 Total methylated C's in Unknown context: 1544651 Total unmethylated C's in CpG context: 12707425 Total unmethylated C's in CHG context: 78981594 Total unmethylated C's in CHH context: 215390285 Total unmethylated C's in Unknown context: 6321823 C methylated in CpG context: 74.9% C methylated in CHG context: 3.6% C methylated in CHH context: 4.5% C methylated in Unknown context (CN or CHN): 19.6% Bismark completed in 0d 11h 1m 54s