Bismark report for: /gscratch/srlab/sr320/data/oakl/zr2096_9_s1_R1_val_1.fq.gz and /gscratch/srlab/sr320/data/oakl/zr2096_9_s1_R2_val_2.fq.gz (version: v0.21.0)
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 14 --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:	31847541
Number of paired-end alignments with a unique best hit:	16106014
Mapping efficiency:	50.6% 
Sequence pairs with no alignments under any condition:	9175850
Sequence pairs did not map uniquely:	6565677
Sequence pairs which were discarded because genomic sequence could not be extracted:	5

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	4344811	((converted) top strand)
GA/CT/CT:	3702414	(complementary to (converted) top strand)
GA/CT/GA:	3705383	(complementary to (converted) bottom strand)
CT/GA/GA:	4353401	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	446185263

Total methylated C's in CpG context:	48195285
Total methylated C's in CHG context:	2775999
Total methylated C's in CHH context:	12261277
Total methylated C's in Unknown context:	1257835

Total unmethylated C's in CpG context:	14395469
Total unmethylated C's in CHG context:	95974288
Total unmethylated C's in CHH context:	272582945
Total unmethylated C's in Unknown context:	5528605

C methylated in CpG context:	77.0%
C methylated in CHG context:	2.8%
C methylated in CHH context:	4.3%
C methylated in unknown context (CN or CHN):	18.5%


Bismark completed in 0d 7h 51m 54s