Bismark report for: zr2096_1_s1_R1_val_1.fq.gz and zr2096_1_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:	91
Mapping efficiency:	9.1% 
Sequence pairs with no alignments under any condition:	864
Sequence pairs did not map uniquely:	45
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:	24	((converted) top strand)
GA/CT/CT:	21	(complementary to (converted) top strand)
GA/CT/GA:	23	(complementary to (converted) bottom strand)
CT/GA/GA:	23	((converted) bottom strand)

Final Cytosine Methylation Report
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Total number of C's analysed:	2420

Total methylated C's in CpG context:	221
Total methylated C's in CHG context:	13
Total methylated C's in CHH context:	34
Total methylated C's in Unknown context:	2


Total unmethylated C's in CpG context:	71
Total unmethylated C's in CHG context:	515
Total unmethylated C's in CHH context:	1566
Total unmethylated C's in Unknown context:	4


C methylated in CpG context:	75.7%
C methylated in CHG context:	2.5%
C methylated in CHH context:	2.1%
C methylated in unknown context (CN or CHN):	33.3%


Bismark completed in 0d 0h 0m 18s