Bismark report for: /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_10_s1_R1_val_1.fq.gz and /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_10_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:	17448883
Number of paired-end alignments with a unique best hit:	9282636
Mapping efficiency:	53.2% 
Sequence pairs with no alignments under any condition:	4524985
Sequence pairs did not map uniquely:	3641262
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:	2365261	((converted) top strand)
GA/CT/CT:	2269368	(complementary to (converted) top strand)
GA/CT/GA:	2275104	(complementary to (converted) bottom strand)
CT/GA/GA:	2372903	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	252303007

Total methylated C's in CpG context:	24797899
Total methylated C's in CHG context:	1458878
Total methylated C's in CHH context:	6698414
Total methylated C's in Unknown context:	649565


Total unmethylated C's in CpG context:	10526009
Total unmethylated C's in CHG context:	54477988
Total unmethylated C's in CHH context:	154343819
Total unmethylated C's in Unknown context:	2848039


C methylated in CpG context:	70.2%
C methylated in CHG context:	2.6%
C methylated in CHH context:	4.2%
C methylated in unknown context (CN or CHN):	18.6%


Bismark completed in 0d 6h 27m 17s