Bismark report for: /gscratch/srlab/sr320/data/oakl/zr2096_10_s1_R1_val_1.fq.gz and /gscratch/srlab/sr320/data/oakl/zr2096_10_s1_R2_val_2.fq.gz (version: v0.19.0)
Bismark was run with Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cvirg-genome/ with the specified options: -q --score-min L,0,-1.2 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500
Option '--directional' specified (default mode): alignments to complementary strands (CTOT, CTOB) were ignored (i.e. not performed)

Final Alignment report
======================
Sequence pairs analysed in total:	17448883
Number of paired-end alignments with a unique best hit:	6101640
Mapping efficiency:	35.0% 
Sequence pairs with no alignments under any condition:	9119335
Sequence pairs did not map uniquely:	2227908
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:	3051408	((converted) top strand)
GA/CT/CT:	0	(complementary to (converted) top strand)
GA/CT/GA:	0	(complementary to (converted) bottom strand)
CT/GA/GA:	3050232	((converted) bottom strand)

Number of alignments to (merely theoretical) complementary strands being rejected in total:	0

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	155361061

Total methylated C's in CpG context:	14429916
Total methylated C's in CHG context:	2478416
Total methylated C's in CHH context:	18074812
Total methylated C's in Unknown context:	901290


Total unmethylated C's in CpG context:	5602290
Total unmethylated C's in CHG context:	28295170
Total unmethylated C's in CHH context:	86480457
Total unmethylated C's in Unknown context:	2099324


C methylated in CpG context:	72.0%
C methylated in CHG context:	8.1%
C methylated in CHH context:	17.3%
C methylated in unknown context (CN or CHN):	30.0%


Bismark completed in 0d 2h 27m 59s