Bismark report for: zr2096_3_s1_R1.fastq.gz and zr2096_3_s1_R2.fastq.gz (version: v0.19.0) 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 --no-mixed --no-discordant --dovetail --maxins 500 Option '--non_directional' specified: alignments to all strands were being performed (OT, OB, CTOT, CTOB) Final Alignment report ====================== Sequence pairs analysed in total: 10000 Number of paired-end alignments with a unique best hit: 5583 Mapping efficiency: 55.8% Sequence pairs with no alignments under any condition: 2628 Sequence pairs did not map uniquely: 1789 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 1386 ((converted) top strand) GA/CT/CT: 1394 (complementary to (converted) top strand) GA/CT/GA: 1415 (complementary to (converted) bottom strand) CT/GA/GA: 1388 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 194605 Total methylated C's in CpG context: 21681 Total methylated C's in CHG context: 1445 Total methylated C's in CHH context: 4620 Total methylated C's in Unknown context: 648 Total unmethylated C's in CpG context: 6661 Total unmethylated C's in CHG context: 43123 Total unmethylated C's in CHH context: 117075 Total unmethylated C's in Unknown context: 2869 C methylated in CpG context: 76.5% C methylated in CHG context: 3.2% C methylated in CHH context: 3.8% C methylated in unknown context (CN or CHN): 18.4% Bismark completed in 0d 0h 0m 28s