Bismark report for: /Volumes/web/nightingales/C_virginica/zr2096_10_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: 17717127 Number of alignments with a unique best hit from the different alignments: 11231576 Mapping efficiency: 63.4% Sequences with no alignments under any condition: 2344949 Sequences did not map uniquely: 4140602 Sequences which were discarded because genomic sequence could not be extracted: 1 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 2635470 ((converted) top strand) CT/GA: 2648518 ((converted) bottom strand) GA/CT: 2969843 (complementary to (converted) top strand) GA/GA: 2977744 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 193910177 Total methylated C's in CpG context: 18669079 Total methylated C's in CHG context: 1470722 Total methylated C's in CHH context: 5197409 Total methylated C's in Unknown context: 747627 Total unmethylated C's in CpG context: 8667337 Total unmethylated C's in CHG context: 42748669 Total unmethylated C's in CHH context: 117156961 Total unmethylated C's in Unknown context: 3140871 C methylated in CpG context: 68.3% C methylated in CHG context: 3.3% C methylated in CHH context: 4.2% C methylated in Unknown context (CN or CHN): 19.2% Bismark completed in 0d 17h 21m 4s