Bismark report for: /gscratch/srlab/sr320/data/oakl/zr2096_7_s1_R1_val_1.fq.gz and /gscratch/srlab/sr320/data/oakl/zr2096_7_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:	29273635
Number of paired-end alignments with a unique best hit:	15119737
Mapping efficiency:	51.6% 
Sequence pairs with no alignments under any condition:	8438168
Sequence pairs did not map uniquely:	5715730
Sequence pairs which were discarded because genomic sequence could not be extracted:	7

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	3843033	((converted) top strand)
GA/CT/CT:	3713941	(complementary to (converted) top strand)
GA/CT/GA:	3714317	(complementary to (converted) bottom strand)
CT/GA/GA:	3848439	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	401269666

Total methylated C's in CpG context:	36888782
Total methylated C's in CHG context:	2315535
Total methylated C's in CHH context:	11270486
Total methylated C's in Unknown context:	1068639


Total unmethylated C's in CpG context:	14076980
Total unmethylated C's in CHG context:	84941638
Total unmethylated C's in CHH context:	251776245
Total unmethylated C's in Unknown context:	4952851


C methylated in CpG context:	72.4%
C methylated in CHG context:	2.7%
C methylated in CHH context:	4.3%
C methylated in unknown context (CN or CHN):	17.7%


Bismark completed in 0d 11h 33m 15s