Bismark report for: /gscratch/srlab/sr320/data/oakl/zr2096_5_s1_R1_val_1.fq.gz and /gscratch/srlab/sr320/data/oakl/zr2096_5_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:	31503281
Number of paired-end alignments with a unique best hit:	16374541
Mapping efficiency:	52.0% 
Sequence pairs with no alignments under any condition:	8772637
Sequence pairs did not map uniquely:	6356103
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:	4233063	((converted) top strand)
GA/CT/CT:	3961266	(complementary to (converted) top strand)
GA/CT/GA:	3951322	(complementary to (converted) bottom strand)
CT/GA/GA:	4228885	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	426940151

Total methylated C's in CpG context:	36700313
Total methylated C's in CHG context:	2371638
Total methylated C's in CHH context:	12917409
Total methylated C's in Unknown context:	1275922


Total unmethylated C's in CpG context:	17093166
Total unmethylated C's in CHG context:	88529768
Total unmethylated C's in CHH context:	269327857
Total unmethylated C's in Unknown context:	5433734


C methylated in CpG context:	68.2%
C methylated in CHG context:	2.6%
C methylated in CHH context:	4.6%
C methylated in unknown context (CN or CHN):	19.0%


Bismark completed in 0d 12h 29m 23s