Bismark report for: /gscratch/srlab/sr320/data/cvirg/6M_R1_val_1.fq.gz and /gscratch/srlab/sr320/data/cvirg/6M_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:	156817982
Number of paired-end alignments with a unique best hit:	87759040
Mapping efficiency:	56.0% 
Sequence pairs with no alignments under any condition:	43018405
Sequence pairs did not map uniquely:	26040537
Sequence pairs which were discarded because genomic sequence could not be extracted:	109

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	21781502	((converted) top strand)
GA/CT/CT:	22074312	(complementary to (converted) top strand)
GA/CT/GA:	22094808	(complementary to (converted) bottom strand)
CT/GA/GA:	21808309	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	3628530531

Total methylated C's in CpG context:	69347460
Total methylated C's in CHG context:	3029600
Total methylated C's in CHH context:	14405917
Total methylated C's in Unknown context:	368349

Total unmethylated C's in CpG context:	443733583
Total unmethylated C's in CHG context:	698908031
Total unmethylated C's in CHH context:	2399105940
Total unmethylated C's in Unknown context:	11131292

C methylated in CpG context:	13.5%
C methylated in CHG context:	0.4%
C methylated in CHH context:	0.6%
C methylated in unknown context (CN or CHN):	3.2%


Bismark completed in 0d 14h 54m 19s