Bismark report for: /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_8_s1_R1_val_1.fq.gz and /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_8_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: 29483218 Number of paired-end alignments with a unique best hit: 5162019 Mapping efficiency: 17.5% Sequence pairs with no alignments under any condition: 21488196 Sequence pairs did not map uniquely: 2833003 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: 1320745 ((converted) top strand) GA/CT/CT: 1271713 (complementary to (converted) top strand) GA/CT/GA: 1258935 (complementary to (converted) bottom strand) CT/GA/GA: 1310626 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 136554467 Total methylated C's in CpG context: 13140416 Total methylated C's in CHG context: 503272 Total methylated C's in CHH context: 1568809 Total methylated C's in Unknown context: 8809 Total unmethylated C's in CpG context: 4475183 Total unmethylated C's in CHG context: 31114019 Total unmethylated C's in CHH context: 85752768 Total unmethylated C's in Unknown context: 84023 C methylated in CpG context: 74.6% C methylated in CHG context: 1.6% C methylated in CHH context: 1.8% C methylated in unknown context (CN or CHN): 9.5% Bismark completed in 0d 3h 7m 47s