Bismark report for: /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_2_s1_R1_val_1.fq.gz and /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_2_s1_R2_val_2.fq.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,-0.2 -p 4 --reorder --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: 1915 Mapping efficiency: 19.1% Sequence pairs with no alignments under any condition: 6886 Sequence pairs did not map uniquely: 1199 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: 508 ((converted) top strand) GA/CT/CT: 456 (complementary to (converted) top strand) GA/CT/GA: 491 (complementary to (converted) bottom strand) CT/GA/GA: 460 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 49228 Total methylated C's in CpG context: 5554 Total methylated C's in CHG context: 186 Total methylated C's in CHH context: 584 Total methylated C's in Unknown context: 6 Total unmethylated C's in CpG context: 1564 Total unmethylated C's in CHG context: 11561 Total unmethylated C's in CHH context: 29779 Total unmethylated C's in Unknown context: 34 C methylated in CpG context: 78.0% C methylated in CHG context: 1.6% C methylated in CHH context: 1.9% C methylated in unknown context (CN or CHN): 15.0% Bismark completed in 0d 0h 0m 28s