Bismark report for: /gscratch/srlab/sr320/data/oakl/zr2096_2_s1_R1_val_1.fq.gz and /gscratch/srlab/sr320/data/oakl/zr2096_2_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:	30325606
Number of paired-end alignments with a unique best hit:	15252038
Mapping efficiency:	50.3% 
Sequence pairs with no alignments under any condition:	8686749
Sequence pairs did not map uniquely:	6386819
Sequence pairs which were discarded because genomic sequence could not be extracted:	3

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	3851551	((converted) top strand)
GA/CT/CT:	3775231	(complementary to (converted) top strand)
GA/CT/GA:	3775326	(complementary to (converted) bottom strand)
CT/GA/GA:	3849927	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	375893936

Total methylated C's in CpG context:	35557561
Total methylated C's in CHG context:	2285641
Total methylated C's in CHH context:	17025048
Total methylated C's in Unknown context:	1564052


Total unmethylated C's in CpG context:	13982978
Total unmethylated C's in CHG context:	79870113
Total unmethylated C's in CHH context:	227172595
Total unmethylated C's in Unknown context:	5094985


C methylated in CpG context:	71.8%
C methylated in CHG context:	2.8%
C methylated in CHH context:	7.0%
C methylated in unknown context (CN or CHN):	23.5%


Bismark completed in 0d 11h 29m 21s