Bismark report for: zr2096_8_s1_R1.fastq.gz and zr2096_8_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: 4805 Mapping efficiency: 48.0% Sequence pairs with no alignments under any condition: 3690 Sequence pairs did not map uniquely: 1505 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: 1178 ((converted) top strand) GA/CT/CT: 1211 (complementary to (converted) top strand) GA/CT/GA: 1179 (complementary to (converted) bottom strand) CT/GA/GA: 1237 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 156859 Total methylated C's in CpG context: 13026 Total methylated C's in CHG context: 1109 Total methylated C's in CHH context: 4711 Total methylated C's in Unknown context: 571 Total unmethylated C's in CpG context: 6649 Total unmethylated C's in CHG context: 34130 Total unmethylated C's in CHH context: 97234 Total unmethylated C's in Unknown context: 2213 C methylated in CpG context: 66.2% C methylated in CHG context: 3.1% C methylated in CHH context: 4.6% C methylated in unknown context (CN or CHN): 20.5% Bismark completed in 0d 0h 0m 26s