Bismark report for: /gscratch/srlab/sr320/data/cvirg/59M_R1_val_1.fq.gz and /gscratch/srlab/sr320/data/cvirg/59M_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:	140047179
Number of paired-end alignments with a unique best hit:	80039790
Mapping efficiency:	57.2% 
Sequence pairs with no alignments under any condition:	34620424
Sequence pairs did not map uniquely:	25386965
Sequence pairs which were discarded because genomic sequence could not be extracted:	110

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	20029357	((converted) top strand)
GA/CT/CT:	19976209	(complementary to (converted) top strand)
GA/CT/GA:	19987409	(complementary to (converted) bottom strand)
CT/GA/GA:	20046705	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	3113845939

Total methylated C's in CpG context:	60813384
Total methylated C's in CHG context:	2325913
Total methylated C's in CHH context:	9784189
Total methylated C's in Unknown context:	247025

Total unmethylated C's in CpG context:	363464595
Total unmethylated C's in CHG context:	577415501
Total unmethylated C's in CHH context:	2100042357
Total unmethylated C's in Unknown context:	9330745

C methylated in CpG context:	14.3%
C methylated in CHG context:	0.4%
C methylated in CHH context:	0.5%
C methylated in unknown context (CN or CHN):	2.6%


Bismark completed in 0d 13h 9m 30s