Bismark report for: /gscratch/scrubbed/yaamini/data/Virginica-MBD/2018-10-17-Trimmed-Files//zr2096_7_s1_R1_val_1.fq.gz and /gscratch/scrubbed/yaamini/data/Virginica-MBD/2018-10-17-Trimmed-Files//zr2096_7_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:	29273635
Number of paired-end alignments with a unique best hit:	15123232
Mapping efficiency:	51.7% 
Sequence pairs with no alignments under any condition:	8438065
Sequence pairs did not map uniquely:	5712338
Sequence pairs which were discarded because genomic sequence could not be extracted:	6

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	3844203	((converted) top strand)
GA/CT/CT:	3715088	(complementary to (converted) top strand)
GA/CT/GA:	3714494	(complementary to (converted) bottom strand)
CT/GA/GA:	3849441	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	401391964

Total methylated C's in CpG context:	36887057
Total methylated C's in CHG context:	2314187
Total methylated C's in CHH context:	11264648
Total methylated C's in Unknown context:	1069033


Total unmethylated C's in CpG context:	14089338
Total unmethylated C's in CHG context:	84945133
Total unmethylated C's in CHH context:	251891601
Total unmethylated C's in Unknown context:	4972076


C methylated in CpG context:	72.4%
C methylated in CHG context:	2.7%
C methylated in CHH context:	4.3%
C methylated in unknown context (CN or CHN):	17.7%


Bismark completed in 0d 11h 9m 54s