Bismark report for: /gscratch/srlab/sr320/data/cvirg/53F_R1_val_1.fq.gz and /gscratch/srlab/sr320/data/cvirg/53F_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:	171116745
Number of paired-end alignments with a unique best hit:	99736023
Mapping efficiency:	58.3% 
Sequence pairs with no alignments under any condition:	47365652
Sequence pairs did not map uniquely:	24015070
Sequence pairs which were discarded because genomic sequence could not be extracted:	1297

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	25110290	((converted) top strand)
GA/CT/CT:	24871801	(complementary to (converted) top strand)
GA/CT/GA:	24748499	(complementary to (converted) bottom strand)
CT/GA/GA:	25004136	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	4213397728

Total methylated C's in CpG context:	63588936
Total methylated C's in CHG context:	2999855
Total methylated C's in CHH context:	12088410
Total methylated C's in Unknown context:	265748

Total unmethylated C's in CpG context:	468154619
Total unmethylated C's in CHG context:	732034413
Total unmethylated C's in CHH context:	2934531495
Total unmethylated C's in Unknown context:	13679528

C methylated in CpG context:	12.0%
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 17h 24m 33s