Bismark report for: /gscratch/srlab/sr320/data/oakl/zr2096_1_s1_R1_val_1.fq.gz and /gscratch/srlab/sr320/data/oakl/zr2096_1_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:	28603346
Number of paired-end alignments with a unique best hit:	8278708
Mapping efficiency:	28.9% 
Sequence pairs with no alignments under any condition:	17321475
Sequence pairs did not map uniquely:	3003163
Sequence pairs which were discarded because genomic sequence could not be extracted:	1

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	2087627	((converted) top strand)
GA/CT/CT:	2089422	(complementary to (converted) top strand)
GA/CT/GA:	2053204	(complementary to (converted) bottom strand)
CT/GA/GA:	2048454	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	200749482

Total methylated C's in CpG context:	16776198
Total methylated C's in CHG context:	1548299
Total methylated C's in CHH context:	15644588
Total methylated C's in Unknown context:	1577296


Total unmethylated C's in CpG context:	7085155
Total unmethylated C's in CHG context:	37129478
Total unmethylated C's in CHH context:	122565764
Total unmethylated C's in Unknown context:	3382097


C methylated in CpG context:	70.3%
C methylated in CHG context:	4.0%
C methylated in CHH context:	11.3%
C methylated in unknown context (CN or CHN):	31.8%


Bismark completed in 0d 7h 22m 23s