Bismark report for: /Volumes/web/nightingales/C_virginica/zr2096_4_s1_R2.fastq.gz (version: v0.19.0)
Option '--non_directional' specified: alignments to all strands were being performed (OT, OB, CTOT, CTOB)
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 --ignore-quals

Final Alignment report
======================
Sequences analysed in total:	10000
Number of alignments with a unique best hit from the different alignments:	6188
Mapping efficiency:	61.9%
Sequences with no alignments under any condition:	1494
Sequences did not map uniquely:	2318
Sequences which were discarded because genomic sequence could not be extracted:	0

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	1384	((converted) top strand)
CT/GA:	1382	((converted) bottom strand)
GA/CT:	1716	(complementary to (converted) top strand)
GA/GA:	1706	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	99874

Total methylated C's in CpG context:	8463
Total methylated C's in CHG context:	657
Total methylated C's in CHH context:	2768
Total methylated C's in Unknown context:	385

Total unmethylated C's in CpG context:	4531
Total unmethylated C's in CHG context:	21673
Total unmethylated C's in CHH context:	61782
Total unmethylated C's in Unknown context:	1781

C methylated in CpG context:	65.1%
C methylated in CHG context:	2.9%
C methylated in CHH context:	4.3%
C methylated in Unknown context (CN or CHN):	17.8%


Bismark completed in 0d 0h 2m 11s