Bismark report for: /gscratch/srlab/sr320/data/cvirg/48M_R1_val_1.fq.gz and /gscratch/srlab/sr320/data/cvirg/48M_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:	202125624
Number of paired-end alignments with a unique best hit:	115530829
Mapping efficiency:	57.2% 
Sequence pairs with no alignments under any condition:	50836754
Sequence pairs did not map uniquely:	35758041
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:	28924082	((converted) top strand)
GA/CT/CT:	28849225	(complementary to (converted) top strand)
GA/CT/GA:	28842857	(complementary to (converted) bottom strand)
CT/GA/GA:	28914533	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	4790942878

Total methylated C's in CpG context:	89079471
Total methylated C's in CHG context:	3760708
Total methylated C's in CHH context:	18396502
Total methylated C's in Unknown context:	414558

Total unmethylated C's in CpG context:	571435071
Total unmethylated C's in CHG context:	921433272
Total unmethylated C's in CHH context:	3186837854
Total unmethylated C's in Unknown context:	14527659

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):	2.8%


Bismark completed in 0d 19h 32m 47s