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Detailed information for vg0906309211:

Variant ID: vg0906309211 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 6309211
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGCCCCACACGACTCTAGCAGAAAAACAAACGAGAAGAACACACGCGCAAGCCTACTAACTGCTCGTCTACTTCTGCGACGGGCCAGGGCGGAAGGTGAG[C/T]
AGTAGCGCATCCTCCATGCTGCCAACGCCAGAGGCTCCCTCCTCCTGAGGAACCACGGGCGCGGGCTCGGCACGAGGGGTCTCGACAAAACAGGTCCATG

Reverse complement sequence

CATGGACCTGTTTTGTCGAGACCCCTCGTGCCGAGCCCGCGCCCGTGGTTCCTCAGGAGGAGGGAGCCTCTGGCGTTGGCAGCATGGAGGATGCGCTACT[G/A]
CTCACCTTCCGCCCTGGCCCGTCGCAGAAGTAGACGAGCAGTTAGTAGGCTTGCGCGTGTGTTCTTCTCGTTTGTTTTTCTGCTAGAGTCGTGTGGGGCA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	72.70%	0.70%	13.33%	13.35%	NA
All Indica	2759	64.10%	1.10%	19.03%	15.84%	NA
All Japonica	1512	87.70%	0.00%	0.86%	11.44%	NA
Aus	269	73.60%	0.00%	26.02%	0.37%	NA
Indica I	595	64.20%	0.70%	22.86%	12.27%	NA
Indica II	465	60.00%	1.10%	13.98%	24.95%	NA
Indica III	913	64.10%	1.00%	20.70%	14.24%	NA
Indica Intermediate	786	66.40%	1.40%	17.18%	15.01%	NA
Temperate Japonica	767	94.80%	0.00%	0.52%	4.69%	NA
Tropical Japonica	504	91.30%	0.00%	0.20%	8.53%	NA
Japonica Intermediate	241	57.70%	0.00%	3.32%	39.00%	NA
VI/Aromatic	96	63.50%	1.00%	17.71%	17.71%	NA
Intermediate	90	90.00%	1.10%	5.56%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0906309211	C -> DEL	N	N	silent_mutation	Average:59.327; most accessible tissue: Minghui63 flag leaf, score: 91.28	N	N	N	N
vg0906309211	C -> T	LOC_Os09g11360.1	intron_variant ; MODIFIER	silent_mutation	Average:59.327; most accessible tissue: Minghui63 flag leaf, score: 91.28	N	N	N	N

Effects Predicted by Deep Convolutional Neural Networks

For each variant, we constructed two sequences that contain the variation site and the sequence around it, differing only in the variation site. We then used Basenji to predict the chromatin accessibility of each tissue for the two sequences, respectively, and scored the effect of the variant by comparing the changes in chromatin accessibility corresponding to the two genotypes in the 1 kb region around the variation site. The effect score was defined as the logarithmic ratio of the predicted chromatin accessibility of the alternative genotype to the value of the reference genotype.

Var ID	Ref	Alt	Root (RT)	Young Leaf (YL)	Flag Leaf (FL)	Young Panicle (YP)	Lemma & Palea (LP)	Stamen & Pistil (SP)
vg0906309211	C	T	-0.01	-0.01	-0.01	-0.01	-0.01	-0.01

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0906309211	2.52E-06	3.73E-06	mr1976_2	Ind_All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251