Bismark report for: /gscratch/srlab/sr320/data/oakl/zr2096_8_s1_R1_val_1.fq.gz and /gscratch/srlab/sr320/data/oakl/zr2096_8_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:	29483218
Number of paired-end alignments with a unique best hit:	14200457
Mapping efficiency:	48.2% 
Sequence pairs with no alignments under any condition:	9943091
Sequence pairs did not map uniquely:	5339670
Sequence pairs which were discarded because genomic sequence could not be extracted:	11

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	3629623	((converted) top strand)
GA/CT/CT:	3487312	(complementary to (converted) top strand)
GA/CT/GA:	3469221	(complementary to (converted) bottom strand)
CT/GA/GA:	3614290	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	362325793

Total methylated C's in CpG context:	29296176
Total methylated C's in CHG context:	2166238
Total methylated C's in CHH context:	13277789
Total methylated C's in Unknown context:	1219151


Total unmethylated C's in CpG context:	14325747
Total unmethylated C's in CHG context:	75728593
Total unmethylated C's in CHH context:	227531250
Total unmethylated C's in Unknown context:	4683321


C methylated in CpG context:	67.2%
C methylated in CHG context:	2.8%
C methylated in CHH context:	5.5%
C methylated in unknown context (CN or CHN):	20.7%


Bismark completed in 0d 11h 1m 55s