Bismark report for: /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_9_s1_R1_val_1.fq.gz and /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_9_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
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Sequence pairs analysed in total:	31847541
Number of paired-end alignments with a unique best hit:	6030681
Mapping efficiency:	18.9% 
Sequence pairs with no alignments under any condition:	22269696
Sequence pairs did not map uniquely:	3547164
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:	1609858	((converted) top strand)
GA/CT/CT:	1407149	(complementary to (converted) top strand)
GA/CT/GA:	1404003	(complementary to (converted) bottom strand)
CT/GA/GA:	1609671	((converted) bottom strand)

Final Cytosine Methylation Report
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Total number of C's analysed:	169474148

Total methylated C's in CpG context:	21090135
Total methylated C's in CHG context:	667737
Total methylated C's in CHH context:	1810307
Total methylated C's in Unknown context:	11426


Total unmethylated C's in CpG context:	4088645
Total unmethylated C's in CHG context:	38795531
Total unmethylated C's in CHH context:	103021793
Total unmethylated C's in Unknown context:	96235


C methylated in CpG context:	83.8%
C methylated in CHG context:	1.7%
C methylated in CHH context:	1.7%
C methylated in unknown context (CN or CHN):	10.6%


Bismark completed in 0d 3h 27m 1s