Bismark report for: /Volumes/web/nightingales/C_virginica/zr2096_6_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:	24237290
Number of alignments with a unique best hit from the different alignments:	15427827
Mapping efficiency:	63.7%
Sequences with no alignments under any condition:	3111552
Sequences did not map uniquely:	5697911
Sequences which were discarded because genomic sequence could not be extracted:	2

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	3844741	((converted) top strand)
CT/GA:	3861066	((converted) bottom strand)
GA/CT:	3858792	(complementary to (converted) top strand)
GA/GA:	3863226	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	250829021

Total methylated C's in CpG context:	23883245
Total methylated C's in CHG context:	1839758
Total methylated C's in CHH context:	7204945
Total methylated C's in Unknown context:	1018995

Total unmethylated C's in CpG context:	9489687
Total unmethylated C's in CHG context:	54793502
Total unmethylated C's in CHH context:	153617884
Total unmethylated C's in Unknown context:	4447030

C methylated in CpG context:	71.6%
C methylated in CHG context:	3.2%
C methylated in CHH context:	4.5%
C methylated in Unknown context (CN or CHN):	18.6%


Bismark completed in 1d 15h 39m 41s