Bismark report for: /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_3_s1_R1_val_1.fq.gz and /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_3_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: 29548753 Number of paired-end alignments with a unique best hit: 15542349 Mapping efficiency: 52.6% Sequence pairs with no alignments under any condition: 7362526 Sequence pairs did not map uniquely: 6643878 Sequence pairs which were discarded because genomic sequence could not be extracted: 2 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 3906974 ((converted) top strand) GA/CT/CT: 3851211 (complementary to (converted) top strand) GA/CT/GA: 3865023 (complementary to (converted) bottom strand) CT/GA/GA: 3919139 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 424899469 Total methylated C's in CpG context: 47524867 Total methylated C's in CHG context: 2298043 Total methylated C's in CHH context: 10743678 Total methylated C's in Unknown context: 1088927 Total unmethylated C's in CpG context: 13919758 Total unmethylated C's in CHG context: 92489635 Total unmethylated C's in CHH context: 257923488 Total unmethylated C's in Unknown context: 5034580 C methylated in CpG context: 77.3% C methylated in CHG context: 2.4% C methylated in CHH context: 4.0% C methylated in unknown context (CN or CHN): 17.8% Bismark completed in 0d 6h 44m 27s