Bismark report for: /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_5_s1_R1_val_1.fq.gz and /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_5_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,-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:	31503281
Number of paired-end alignments with a unique best hit:	16377060
Mapping efficiency:	52.0% 
Sequence pairs with no alignments under any condition:	8772590
Sequence pairs did not map uniquely:	6353631
Sequence pairs which were discarded because genomic sequence could not be extracted:	5

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	4233791	((converted) top strand)
GA/CT/CT:	3962037	(complementary to (converted) top strand)
GA/CT/GA:	3951534	(complementary to (converted) bottom strand)
CT/GA/GA:	4229693	((converted) bottom strand)

Final Cytosine Methylation Report
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Total number of C's analysed:	427057721

Total methylated C's in CpG context:	36699636
Total methylated C's in CHG context:	2370188
Total methylated C's in CHH context:	12902291
Total methylated C's in Unknown context:	1275308


Total unmethylated C's in CpG context:	17105060
Total unmethylated C's in CHG context:	88534839
Total unmethylated C's in CHH context:	269445707
Total unmethylated C's in Unknown context:	5454992


C methylated in CpG context:	68.2%
C methylated in CHG context:	2.6%
C methylated in CHH context:	4.6%
C methylated in unknown context (CN or CHN):	18.9%


Bismark completed in 0d 7h 27m 45s