Bismark report for: /gscratch/srlab/sr320/data/cvirg/50F_R1_val_1.fq.gz and /gscratch/srlab/sr320/data/cvirg/50F_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:	147179212
Number of paired-end alignments with a unique best hit:	83381318
Mapping efficiency:	56.7% 
Sequence pairs with no alignments under any condition:	45245169
Sequence pairs did not map uniquely:	18552725
Sequence pairs which were discarded because genomic sequence could not be extracted:	502

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	20941531	((converted) top strand)
GA/CT/CT:	20857716	(complementary to (converted) top strand)
GA/CT/GA:	20742134	(complementary to (converted) bottom strand)
CT/GA/GA:	20839435	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	3568167604

Total methylated C's in CpG context:	54317296
Total methylated C's in CHG context:	2629468
Total methylated C's in CHH context:	11006199
Total methylated C's in Unknown context:	248689

Total unmethylated C's in CpG context:	395052270
Total unmethylated C's in CHG context:	624289769
Total unmethylated C's in CHH context:	2480872602
Total unmethylated C's in Unknown context:	11791014

C methylated in CpG context:	12.1%
C methylated in CHG context:	0.4%
C methylated in CHH context:	0.4%
C methylated in unknown context (CN or CHN):	2.1%


Bismark completed in 0d 14h 52m 10s