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 '--non_directional' specified: alignments to all strands were being performed (OT, OB, CTOT, CTOB)

Final Alignment report
======================
Sequence pairs analysed in total:	17448883
Number of paired-end alignments with a unique best hit:	9281826
Mapping efficiency:	53.2% 
Sequence pairs with no alignments under any condition:	4524878
Sequence pairs did not map uniquely:	3642179
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:	2365021	((converted) top strand)
GA/CT/CT:	2269427	(complementary to (converted) top strand)
GA/CT/GA:	2275081	(complementary to (converted) bottom strand)
CT/GA/GA:	2372297	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	252267854

Total methylated C's in CpG context:	24800640
Total methylated C's in CHG context:	1459772
Total methylated C's in CHH context:	6704299
Total methylated C's in Unknown context:	649166


Total unmethylated C's in CpG context:	10519584
Total unmethylated C's in CHG context:	54484161
Total unmethylated C's in CHH context:	154299398
Total unmethylated C's in Unknown context:	2835983


C methylated in CpG context:	70.2%
C methylated in CHG context:	2.6%
C methylated in CHH context:	4.2%
C methylated in unknown context (CN or CHN):	18.6%


Bismark completed in 0d 7h 3m 30s