Bismark report for: /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_6_s1_R1_val_1.fq.gz and /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_6_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,-1.2 -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: 23909493 Number of paired-end alignments with a unique best hit: 13016030 Mapping efficiency: 54.4% Sequence pairs with no alignments under any condition: 5434045 Sequence pairs did not map uniquely: 5459418 Sequence pairs which were discarded because genomic sequence could not be extracted: 1 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 3414853 ((converted) top strand) GA/CT/CT: 3092674 (complementary to (converted) top strand) GA/CT/GA: 3093838 (complementary to (converted) bottom strand) CT/GA/GA: 3414664 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 332065337 Total methylated C's in CpG context: 32090090 Total methylated C's in CHG context: 1709783 Total methylated C's in CHH context: 9696641 Total methylated C's in Unknown context: 935583 Total unmethylated C's in CpG context: 11442690 Total unmethylated C's in CHG context: 70560142 Total unmethylated C's in CHH context: 206565991 Total unmethylated C's in Unknown context: 4259145 C methylated in CpG context: 73.7% C methylated in CHG context: 2.4% C methylated in CHH context: 4.5% C methylated in unknown context (CN or CHN): 18.0% Bismark completed in 0d 5h 34m 21s