Bismark report for: /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_10_s1_R1.fastq.gz and /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_10_s1_R2.fastq.gz (version: v0.19.0)
Bismark was run with Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Cvirg/Bismark_genome/ with the specified options: -q --score-min L,0,-1.2 --ignore-quals --no-mixed --no-discordant --dovetail --minins 100 --maxins 500
Option '--non_directional' specified: alignments to all strands were being performed (OT, OB, CTOT, CTOB)

Final Alignment report
======================
Sequence pairs analysed in total:	17717127
Number of paired-end alignments with a unique best hit:	6293704
Mapping efficiency:	35.5% 
Sequence pairs with no alignments under any condition:	9714892
Sequence pairs did not map uniquely:	1708531
Sequence pairs which were discarded because genomic sequence could not be extracted:	0

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	1601646	((converted) top strand)
GA/CT/CT:	1537591	(complementary to (converted) top strand)
GA/CT/GA:	1548913	(complementary to (converted) bottom strand)
CT/GA/GA:	1605554	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	232453732

Total methylated C's in CpG context:	22151409
Total methylated C's in CHG context:	1632227
Total methylated C's in CHH context:	5841216
Total methylated C's in Unknown context:	707839


Total unmethylated C's in CpG context:	10405571
Total unmethylated C's in CHG context:	50198281
Total unmethylated C's in CHH context:	142225028
Total unmethylated C's in Unknown context:	2858024


C methylated in CpG context:	68.0%
C methylated in CHG context:	3.1%
C methylated in CHH context:	3.9%
C methylated in unknown context (CN or CHN):	19.9%


Bismark completed in 0d 3h 34m 55s