Bismark report for: /gscratch/scrubbed/yaamini/data/Virginica-MBD/2018-10-17-Trimmed-Files//zr2096_8_s1_R1_val_1.fq.gz and /gscratch/scrubbed/yaamini/data/Virginica-MBD/2018-10-17-Trimmed-Files//zr2096_8_s1_R2_val_2.fq.gz (version: v0.19.0) Bismark was run with Bowtie 2 against the bisulfite genome of /gscratch/scrubbed/yaamini/data/Virginica-MBD/2018-04-27-Bismark-Inputs/ with the specified options: -q --score-min L,0,-1.2 -p 28 --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: 14200416 Mapping efficiency: 48.2% Sequence pairs with no alignments under any condition: 9943053 Sequence pairs did not map uniquely: 5339749 Sequence pairs which were discarded because genomic sequence could not be extracted: 11 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 3629946 ((converted) top strand) GA/CT/CT: 3487296 (complementary to (converted) top strand) GA/CT/GA: 3468647 (complementary to (converted) bottom strand) CT/GA/GA: 3614516 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 362392795 Total methylated C's in CpG context: 29294128 Total methylated C's in CHG context: 2164397 Total methylated C's in CHH context: 13260103 Total methylated C's in Unknown context: 1218115 Total unmethylated C's in CpG context: 14337861 Total unmethylated C's in CHG context: 75732890 Total unmethylated C's in CHH context: 227603416 Total unmethylated C's in Unknown context: 4698419 C methylated in CpG context: 67.1% C methylated in CHG context: 2.8% C methylated in CHH context: 5.5% C methylated in unknown context (CN or CHN): 20.6% Bismark completed in 0d 10h 28m 25s