Bismark report for: /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_5_s1_R1.fastq.gz and /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_5_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:	31778715
Number of paired-end alignments with a unique best hit:	10309461
Mapping efficiency:	32.4% 
Sequence pairs with no alignments under any condition:	18728694
Sequence pairs did not map uniquely:	2740560
Sequence pairs which were discarded because genomic sequence could not be extracted:	5

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	2677514	((converted) top strand)
GA/CT/CT:	2476905	(complementary to (converted) top strand)
GA/CT/GA:	2486673	(complementary to (converted) bottom strand)
CT/GA/GA:	2668364	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	370441524

Total methylated C's in CpG context:	30590802
Total methylated C's in CHG context:	2478038
Total methylated C's in CHH context:	10020162
Total methylated C's in Unknown context:	1213895


Total unmethylated C's in CpG context:	15985714
Total unmethylated C's in CHG context:	76625684
Total unmethylated C's in CHH context:	234741124
Total unmethylated C's in Unknown context:	5096608


C methylated in CpG context:	65.7%
C methylated in CHG context:	3.1%
C methylated in CHH context:	4.1%
C methylated in unknown context (CN or CHN):	19.2%


Bismark completed in 0d 6h 17m 29s