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 '--directional' specified (default mode): alignments to complementary strands (CTOT, CTOB) were ignored (i.e. not performed)

Final Alignment report
======================
Sequence pairs analysed in total:	29548753
Number of paired-end alignments with a unique best hit:	10380653
Mapping efficiency:	35.1% 
Sequence pairs with no alignments under any condition:	15079334
Sequence pairs did not map uniquely:	4088766
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:	5195217	((converted) top strand)
GA/CT/CT:	0	(complementary to (converted) top strand)
GA/CT/GA:	0	(complementary to (converted) bottom strand)
CT/GA/GA:	5185435	((converted) bottom strand)

Number of alignments to (merely theoretical) complementary strands being rejected in total:	0

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	262116982

Total methylated C's in CpG context:	27411098
Total methylated C's in CHG context:	4352030
Total methylated C's in CHH context:	31743267
Total methylated C's in Unknown context:	1620528


Total unmethylated C's in CpG context:	7451747
Total unmethylated C's in CHG context:	47342719
Total unmethylated C's in CHH context:	143816121
Total unmethylated C's in Unknown context:	3735520


C methylated in CpG context:	78.6%
C methylated in CHG context:	8.4%
C methylated in CHH context:	18.1%
C methylated in unknown context (CN or CHN):	30.3%


Bismark completed in 0d 4h 8m 6s