Bismark report for: /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_2_s1_R1.fastq.gz and /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_2_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:	30798582
Number of paired-end alignments with a unique best hit:	7879875
Mapping efficiency:	25.6% 
Sequence pairs with no alignments under any condition:	20682061
Sequence pairs did not map uniquely:	2236646
Sequence pairs which were discarded because genomic sequence could not be extracted:	1

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	1988714	((converted) top strand)
GA/CT/CT:	1934508	(complementary to (converted) top strand)
GA/CT/GA:	1961754	(complementary to (converted) bottom strand)
CT/GA/GA:	1994898	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	282047529

Total methylated C's in CpG context:	25969563
Total methylated C's in CHG context:	1938729
Total methylated C's in CHH context:	9023855
Total methylated C's in Unknown context:	934954


Total unmethylated C's in CpG context:	11825530
Total unmethylated C's in CHG context:	61284539
Total unmethylated C's in CHH context:	172005313
Total unmethylated C's in Unknown context:	3930167


C methylated in CpG context:	68.7%
C methylated in CHG context:	3.1%
C methylated in CHH context:	5.0%
C methylated in unknown context (CN or CHN):	19.2%


Bismark completed in 0d 5h 29m 29s