Bismark report for: zr2096_10_s1_R1_val_1.fq.gz and zr2096_10_s1_R2_val_2.fq.gz (version: v0.19.0)
Bismark was run with Bowtie 2 against the bisulfite genome of /Volumes/Serine/wd/18-03-15/genome/ with the specified options: -q --score-min L,0,-1.2 -p 4 --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:	1000000
Number of paired-end alignments with a unique best hit:	532162
Mapping efficiency:	53.2% 
Sequence pairs with no alignments under any condition:	258809
Sequence pairs did not map uniquely:	209029
Sequence pairs which were discarded because genomic sequence could not be extracted:	0

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	133939	((converted) top strand)
GA/CT/CT:	131970	(complementary to (converted) top strand)
GA/CT/GA:	132144	(complementary to (converted) bottom strand)
CT/GA/GA:	134109	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	14507114

Total methylated C's in CpG context:	1421648
Total methylated C's in CHG context:	83788
Total methylated C's in CHH context:	382029
Total methylated C's in Unknown context:	37110


Total unmethylated C's in CpG context:	604367
Total unmethylated C's in CHG context:	3125846
Total unmethylated C's in CHH context:	8889436
Total unmethylated C's in Unknown context:	164807


C methylated in CpG context:	70.2%
C methylated in CHG context:	2.6%
C methylated in CHH context:	4.1%
C methylated in unknown context (CN or CHN):	18.4%


Bismark completed in 0d 0h 10m 36s