Bismark report for: zr2096_4_s1_R1.fastq.gz and zr2096_4_s1_R2.fastq.gz (version: v0.19.0)
Bismark was run with Bowtie 2 against the bisulfite genome of /Users/yaamini/Documents/project-virginica-oa/analyses/2018-04-27-Bismark/2018-04-27-Bismark-Inputs/ with the specified options: -q --score-min L,0,-1.2 --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
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Sequence pairs analysed in total:	10000
Number of paired-end alignments with a unique best hit:	5532
Mapping efficiency:	55.3% 
Sequence pairs with no alignments under any condition:	2681
Sequence pairs did not map uniquely:	1787
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:	1439	((converted) top strand)
GA/CT/CT:	1326	(complementary to (converted) top strand)
GA/CT/GA:	1325	(complementary to (converted) bottom strand)
CT/GA/GA:	1442	((converted) bottom strand)

Final Cytosine Methylation Report
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Total number of C's analysed:	177679

Total methylated C's in CpG context:	15435
Total methylated C's in CHG context:	1155
Total methylated C's in CHH context:	5016
Total methylated C's in Unknown context:	595


Total unmethylated C's in CpG context:	7999
Total unmethylated C's in CHG context:	38807
Total unmethylated C's in CHH context:	109267
Total unmethylated C's in Unknown context:	2741


C methylated in CpG context:	65.9%
C methylated in CHG context:	2.9%
C methylated in CHH context:	4.4%
C methylated in unknown context (CN or CHN):	17.8%


Bismark completed in 0d 0h 0m 26s