Bismark report for: /gscratch/srlab/sr320/data/cvirg/29F_R1_val_1.fq.gz and /gscratch/srlab/sr320/data/cvirg/29F_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:	137641794
Number of paired-end alignments with a unique best hit:	78897899
Mapping efficiency:	57.3% 
Sequence pairs with no alignments under any condition:	39744516
Sequence pairs did not map uniquely:	18999379
Sequence pairs which were discarded because genomic sequence could not be extracted:	394

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	19767756	((converted) top strand)
GA/CT/CT:	19760348	(complementary to (converted) top strand)
GA/CT/GA:	19683219	(complementary to (converted) bottom strand)
CT/GA/GA:	19686182	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	3335365003

Total methylated C's in CpG context:	49477481
Total methylated C's in CHG context:	2353635
Total methylated C's in CHH context:	9844711
Total methylated C's in Unknown context:	215328

Total unmethylated C's in CpG context:	373680681
Total unmethylated C's in CHG context:	582136274
Total unmethylated C's in CHH context:	2317872221
Total unmethylated C's in Unknown context:	10880597

C methylated in CpG context:	11.7%
C methylated in CHG context:	0.4%
C methylated in CHH context:	0.4%
C methylated in unknown context (CN or CHN):	1.9%


Bismark completed in 0d 13h 54m 32s