Bismark report for: /Volumes/web/nightingales/C_virginica/zr2096_1_s1_R1.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:	3083
Mapping efficiency:	30.8%
Sequences with no alignments under any condition:	5801
Sequences did not map uniquely:	1116
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:	723	((converted) top strand)
CT/GA:	759	((converted) bottom strand)
GA/CT:	808	(complementary to (converted) top strand)
GA/GA:	793	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	50039

Total methylated C's in CpG context:	4195
Total methylated C's in CHG context:	390
Total methylated C's in CHH context:	2635
Total methylated C's in Unknown context:	322

Total unmethylated C's in CpG context:	2109
Total unmethylated C's in CHG context:	10153
Total unmethylated C's in CHH context:	30557
Total unmethylated C's in Unknown context:	1075

C methylated in CpG context:	66.5%
C methylated in CHG context:	3.7%
C methylated in CHH context:	7.9%
C methylated in Unknown context (CN or CHN):	23.0%


Bismark completed in 0d 0h 1m 1s