Bismark report for: /gscratch/srlab/sr320/data/oakl/zr2096_6_s1_R1_val_1.fq.gz and /gscratch/srlab/sr320/data/oakl/zr2096_6_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 '--non_directional' specified: alignments to all strands were being performed (OT, OB, CTOT, CTOB)

Final Alignment report
======================
Sequence pairs analysed in total:	23909493
Number of paired-end alignments with a unique best hit:	13017036
Mapping efficiency:	54.4% 
Sequence pairs with no alignments under any condition:	5434131
Sequence pairs did not map uniquely:	5458326
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:	3415013	((converted) top strand)
GA/CT/CT:	3092677	(complementary to (converted) top strand)
GA/CT/GA:	3094459	(complementary to (converted) bottom strand)
CT/GA/GA:	3414886	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	332041882

Total methylated C's in CpG context:	32094262
Total methylated C's in CHG context:	1710680
Total methylated C's in CHH context:	9705844
Total methylated C's in Unknown context:	935879


Total unmethylated C's in CpG context:	11436395
Total unmethylated C's in CHG context:	70568701
Total unmethylated C's in CHH context:	206526000
Total unmethylated C's in Unknown context:	4247676


C methylated in CpG context:	73.7%
C methylated in CHG context:	2.4%
C methylated in CHH context:	4.5%
C methylated in unknown context (CN or CHN):	18.1%


Bismark completed in 0d 9h 44m 58s