Bismark report for: /gscratch/srlab/sr320/data/cvirg/77F_R1_val_1.fq.gz and /gscratch/srlab/sr320/data/cvirg/77F_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:	183300828
Number of paired-end alignments with a unique best hit:	105710132
Mapping efficiency:	57.7% 
Sequence pairs with no alignments under any condition:	49753928
Sequence pairs did not map uniquely:	27836768
Sequence pairs which were discarded because genomic sequence could not be extracted:	1428

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	26698380	((converted) top strand)
GA/CT/CT:	26560878	(complementary to (converted) top strand)
GA/CT/GA:	26145268	(complementary to (converted) bottom strand)
CT/GA/GA:	26304178	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	4419317856

Total methylated C's in CpG context:	66262743
Total methylated C's in CHG context:	3100353
Total methylated C's in CHH context:	12655064
Total methylated C's in Unknown context:	288225

Total unmethylated C's in CpG context:	507907192
Total unmethylated C's in CHG context:	789148399
Total unmethylated C's in CHH context:	3040244105
Total unmethylated C's in Unknown context:	13811814

C methylated in CpG context:	11.5%
C methylated in CHG context:	0.4%
C methylated in CHH context:	0.4%
C methylated in unknown context (CN or CHN):	2.0%


Bismark completed in 0d 18h 10m 2s