Bismark report for: /gscratch/srlab/sr320/data/cvirg/31M_R1_val_1.fq.gz and /gscratch/srlab/sr320/data/cvirg/31M_R2_val_2.fq.gz (version: v0.22.3)
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,-0.6 -p 4 --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:	141797876
Number of paired-end alignments with a unique best hit:	83818940
Mapping efficiency:	59.1% 
Sequence pairs with no alignments under any condition:	35155949
Sequence pairs did not map uniquely:	22822987
Sequence pairs which were discarded because genomic sequence could not be extracted:	62

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	20896957	((converted) top strand)
GA/CT/CT:	21003842	(complementary to (converted) top strand)
GA/CT/GA:	21013523	(complementary to (converted) bottom strand)
CT/GA/GA:	20904556	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	3471808061

Total methylated C's in CpG context:	63220038
Total methylated C's in CHG context:	2486404
Total methylated C's in CHH context:	10975824
Total methylated C's in Unknown context:	286319

Total unmethylated C's in CpG context:	400980153
Total unmethylated C's in CHG context:	630300848
Total unmethylated C's in CHH context:	2363844794
Total unmethylated C's in Unknown context:	10200137

C methylated in CpG context:	13.6%
C methylated in CHG context:	0.4%
C methylated in CHH context:	0.5%
C methylated in unknown context (CN or CHN):	2.7%


Bismark completed in 0d 14h 17m 51s