Bismark report for: /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_4_s1_R1_val_1.fq.gz and /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_4_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:	23970516
Number of paired-end alignments with a unique best hit:	12995901
Mapping efficiency:	54.2% 
Sequence pairs with no alignments under any condition:	5579694
Sequence pairs did not map uniquely:	5394921
Sequence pairs which were discarded because genomic sequence could not be extracted:	2

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	3325378	((converted) top strand)
GA/CT/CT:	3162868	(complementary to (converted) top strand)
GA/CT/GA:	3171036	(complementary to (converted) bottom strand)
CT/GA/GA:	3336617	((converted) bottom strand)

Final Cytosine Methylation Report
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Total number of C's analysed:	327201316

Total methylated C's in CpG context:	28026421
Total methylated C's in CHG context:	1662436
Total methylated C's in CHH context:	9876129
Total methylated C's in Unknown context:	887156


Total unmethylated C's in CpG context:	13940071
Total unmethylated C's in CHG context:	69726438
Total unmethylated C's in CHH context:	203969821
Total unmethylated C's in Unknown context:	4128531


C methylated in CpG context:	66.8%
C methylated in CHG context:	2.3%
C methylated in CHH context:	4.6%
C methylated in unknown context (CN or CHN):	17.7%


Bismark completed in 0d 5h 30m 55s