Bismark report for: /gscratch/scrubbed/yaamini/data/Virginica-MBD/2018-10-17-Trimmed-Files//zr2096_2_s1_R1_val_1.fq.gz and /gscratch/scrubbed/yaamini/data/Virginica-MBD/2018-10-17-Trimmed-Files//zr2096_2_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: 30325606 Number of paired-end alignments with a unique best hit: 15247793 Mapping efficiency: 50.3% Sequence pairs with no alignments under any condition: 8686774 Sequence pairs did not map uniquely: 6391039 Sequence pairs which were discarded because genomic sequence could not be extracted: 3 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 3850832 ((converted) top strand) GA/CT/CT: 3774008 (complementary to (converted) top strand) GA/CT/GA: 3773813 (complementary to (converted) bottom strand) CT/GA/GA: 3849137 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 375896419 Total methylated C's in CpG context: 35550304 Total methylated C's in CHG context: 2282737 Total methylated C's in CHH context: 16987048 Total methylated C's in Unknown context: 1561533 Total unmethylated C's in CpG context: 13991251 Total unmethylated C's in CHG context: 79870209 Total unmethylated C's in CHH context: 227214870 Total unmethylated C's in Unknown context: 5108826 C methylated in CpG context: 71.8% C methylated in CHG context: 2.8% C methylated in CHH context: 7.0% C methylated in unknown context (CN or CHN): 23.4% Bismark completed in 0d 11h 2m 53s