Bismark report for: /gscratch/srlab/sr320/data/cvirg/16F_R1_val_1.fq.gz and /gscratch/srlab/sr320/data/cvirg/16F_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:	184170994
Number of paired-end alignments with a unique best hit:	103096144
Mapping efficiency:	56.0% 
Sequence pairs with no alignments under any condition:	53479707
Sequence pairs did not map uniquely:	27595143
Sequence pairs which were discarded because genomic sequence could not be extracted:	342

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	25858184	((converted) top strand)
GA/CT/CT:	25751911	(complementary to (converted) top strand)
GA/CT/GA:	25694337	(complementary to (converted) bottom strand)
CT/GA/GA:	25791370	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	4112186084

Total methylated C's in CpG context:	67140496
Total methylated C's in CHG context:	3202091
Total methylated C's in CHH context:	13160640
Total methylated C's in Unknown context:	286211

Total unmethylated C's in CpG context:	470893717
Total unmethylated C's in CHG context:	734473042
Total unmethylated C's in CHH context:	2823316098
Total unmethylated C's in Unknown context:	13163858

C methylated in CpG context:	12.5%
C methylated in CHG context:	0.4%
C methylated in CHH context:	0.5%
C methylated in unknown context (CN or CHN):	2.1%


Bismark completed in 0d 17h 35m 50s