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:	24341968
Number of alignments with a unique best hit from the different alignments:	15266792
Mapping efficiency:	62.7%
Sequences with no alignments under any condition:	3502517
Sequences did not map uniquely:	5572659
Sequences which were discarded because genomic sequence could not be extracted:	8

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	3473421	((converted) top strand)
CT/GA:	3483033	((converted) bottom strand)
GA/CT:	4147234	(complementary to (converted) top strand)
GA/GA:	4163096	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	245364335

Total methylated C's in CpG context:	20716861
Total methylated C's in CHG context:	1725952
Total methylated C's in CHH context:	6966764
Total methylated C's in Unknown context:	893665

Total unmethylated C's in CpG context:	11250057
Total unmethylated C's in CHG context:	53936811
Total unmethylated C's in CHH context:	150767890
Total unmethylated C's in Unknown context:	4262000

C methylated in CpG context:	64.8%
C methylated in CHG context:	3.1%
C methylated in CHH context:	4.4%
C methylated in Unknown context (CN or CHN):	17.3%


Bismark completed in 1d 5h 19m 47s