Bismark report for: /Volumes/web/nightingales/C_virginica/zr2096_5_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:	31778715
Number of alignments with a unique best hit from the different alignments:	19730827
Mapping efficiency:	62.1%
Sequences with no alignments under any condition:	5053315
Sequences did not map uniquely:	6994573
Sequences which were discarded because genomic sequence could not be extracted:	25

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	4704514	((converted) top strand)
CT/GA:	4707771	((converted) bottom strand)
GA/CT:	5166758	(complementary to (converted) top strand)
GA/GA:	5151759	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	328798878

Total methylated C's in CpG context:	28007894
Total methylated C's in CHG context:	2440790
Total methylated C's in CHH context:	9555686
Total methylated C's in Unknown context:	1397495

Total unmethylated C's in CpG context:	14164169
Total unmethylated C's in CHG context:	70203884
Total unmethylated C's in CHH context:	204426455
Total unmethylated C's in Unknown context:	5853556

C methylated in CpG context:	66.4%
C methylated in CHG context:	3.4%
C methylated in CHH context:	4.5%
C methylated in Unknown context (CN or CHN):	19.3%


Bismark completed in 1d 9h 3m 34s