Bismark report for: /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_1_s1_R1_val_1.fq.gz and /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_1_s1_R2_val_2.fq.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,-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:	28603346
Number of paired-end alignments with a unique best hit:	2299993
Mapping efficiency:	8.0% 
Sequence pairs with no alignments under any condition:	24953333
Sequence pairs did not map uniquely:	1350020
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:	572719	((converted) top strand)
GA/CT/CT:	575468	(complementary to (converted) top strand)
GA/CT/GA:	578504	(complementary to (converted) bottom strand)
CT/GA/GA:	573302	((converted) bottom strand)

Final Cytosine Methylation Report
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Total number of C's analysed:	62919883

Total methylated C's in CpG context:	6858656
Total methylated C's in CHG context:	194650
Total methylated C's in CHH context:	664908
Total methylated C's in Unknown context:	4639


Total unmethylated C's in CpG context:	1788453
Total unmethylated C's in CHG context:	14078045
Total unmethylated C's in CHH context:	39335171
Total unmethylated C's in Unknown context:	39895


C methylated in CpG context:	79.3%
C methylated in CHG context:	1.4%
C methylated in CHH context:	1.7%
C methylated in unknown context (CN or CHN):	10.4%


Bismark completed in 0d 2h 18m 4s