Bismark report for: /Volumes/web/nightingales/C_virginica/zr2096_2_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:	30798582
Number of alignments with a unique best hit from the different alignments:	16947236
Mapping efficiency:	55.0%
Sequences with no alignments under any condition:	7672436
Sequences did not map uniquely:	6178910
Sequences which were discarded because genomic sequence could not be extracted:	5

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	4124744	((converted) top strand)
CT/GA:	4152670	((converted) bottom strand)
GA/CT:	4327789	(complementary to (converted) top strand)
GA/GA:	4342028	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	271024981

Total methylated C's in CpG context:	25747003
Total methylated C's in CHG context:	2080992
Total methylated C's in CHH context:	9553145
Total methylated C's in Unknown context:	1213922

Total unmethylated C's in CpG context:	11120086
Total unmethylated C's in CHG context:	60523320
Total unmethylated C's in CHH context:	162000435
Total unmethylated C's in Unknown context:	4791818

C methylated in CpG context:	69.8%
C methylated in CHG context:	3.3%
C methylated in CHH context:	5.6%
C methylated in Unknown context (CN or CHN):	20.2%


Bismark completed in 0d 13h 59m 27s