Bismark report for: zr2096_5_s1_R1_val_1.fq.gz and zr2096_5_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:	520106
Mapping efficiency:	52.0% 
Sequence pairs with no alignments under any condition:	278464
Sequence pairs did not map uniquely:	201430
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:	134098	((converted) top strand)
GA/CT/CT:	126227	(complementary to (converted) top strand)
GA/CT/GA:	126218	(complementary to (converted) bottom strand)
CT/GA/GA:	133563	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	13613606

Total methylated C's in CpG context:	1168935
Total methylated C's in CHG context:	74696
Total methylated C's in CHH context:	406740
Total methylated C's in Unknown context:	40389


Total unmethylated C's in CpG context:	543270
Total unmethylated C's in CHG context:	2814533
Total unmethylated C's in CHH context:	8605432
Total unmethylated C's in Unknown context:	174268


C methylated in CpG context:	68.3%
C methylated in CHG context:	2.6%
C methylated in CHH context:	4.5%
C methylated in unknown context (CN or CHN):	18.8%


Bismark completed in 0d 0h 9m 58s