Bismark report for: /gscratch/srlab/sr320/data/oakl/zr2096_3_s1_R1_val_1.fq.gz and /gscratch/srlab/sr320/data/oakl/zr2096_3_s1_R2_val_2.fq.gz (version: v0.19.0)
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,-1.2 -p 28 --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:	29548753
Number of paired-end alignments with a unique best hit:	15538532
Mapping efficiency:	52.6% 
Sequence pairs with no alignments under any condition:	7362629
Sequence pairs did not map uniquely:	6647592
Sequence pairs which were discarded because genomic sequence could not be extracted:	2

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	3905783	((converted) top strand)
GA/CT/CT:	3850463	(complementary to (converted) top strand)
GA/CT/GA:	3864345	(complementary to (converted) bottom strand)
CT/GA/GA:	3917939	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	424766405

Total methylated C's in CpG context:	47521990
Total methylated C's in CHG context:	2299427
Total methylated C's in CHH context:	10754385
Total methylated C's in Unknown context:	1088578


Total unmethylated C's in CpG context:	13905252
Total unmethylated C's in CHG context:	92474489
Total unmethylated C's in CHH context:	257810862
Total unmethylated C's in Unknown context:	5012717


C methylated in CpG context:	77.4%
C methylated in CHG context:	2.4%
C methylated in CHH context:	4.0%
C methylated in unknown context (CN or CHN):	17.8%


Bismark completed in 0d 11h 51m 57s