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 /Users/sr320/Dropbox/wd/18-03-15/genome/ with the specified options: -q --score-min L,0,-0.2 -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:	1000
Number of paired-end alignments with a unique best hit:	182
Mapping efficiency:	18.2% 
Sequence pairs with no alignments under any condition:	722
Sequence pairs did not map uniquely:	96
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:	43	((converted) top strand)
GA/CT/CT:	46	(complementary to (converted) top strand)
GA/CT/GA:	44	(complementary to (converted) bottom strand)
CT/GA/GA:	49	((converted) bottom strand)

Final Cytosine Methylation Report
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Total number of C's analysed:	4989

Total methylated C's in CpG context:	525
Total methylated C's in CHG context:	18
Total methylated C's in CHH context:	35
Total methylated C's in Unknown context:	0


Total unmethylated C's in CpG context:	126
Total unmethylated C's in CHG context:	1129
Total unmethylated C's in CHH context:	3156
Total unmethylated C's in Unknown context:	0


C methylated in CpG context:	80.6%
C methylated in CHG context:	1.6%
C methylated in CHH context:	1.1%
Can't determine percentage of methylated Cs in unknown context (CN or CHN) if value was 0


Bismark completed in 0d 0h 0m 19s