Bismark report for: /gscratch/srlab/sr320/data/cvirg/13M_R1_val_1.fq.gz and /gscratch/srlab/sr320/data/cvirg/13M_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:	217295607
Number of paired-end alignments with a unique best hit:	124898218
Mapping efficiency:	57.5% 
Sequence pairs with no alignments under any condition:	57467614
Sequence pairs did not map uniquely:	34929775
Sequence pairs which were discarded because genomic sequence could not be extracted:	132

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	31254632	((converted) top strand)
GA/CT/CT:	31176521	(complementary to (converted) top strand)
GA/CT/GA:	31189603	(complementary to (converted) bottom strand)
CT/GA/GA:	31277330	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	5245651403

Total methylated C's in CpG context:	92402811
Total methylated C's in CHG context:	3795552
Total methylated C's in CHH context:	15373578
Total methylated C's in Unknown context:	422443

Total unmethylated C's in CpG context:	616600861
Total unmethylated C's in CHG context:	959301177
Total unmethylated C's in CHH context:	3558177424
Total unmethylated C's in Unknown context:	16442872

C methylated in CpG context:	13.0%
C methylated in CHG context:	0.4%
C methylated in CHH context:	0.4%
C methylated in unknown context (CN or CHN):	2.5%


Bismark completed in 0d 21h 30m 9s