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Detailed information for vg0328953433:

Variant ID: vg0328953433 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 28953433
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.76, A: 0.24, others allele: 0.00, population size: 96. )

Flanking Sequence (100 bp) in Reference Genome:

TTTCTCCCGACTCCCCTCATGCCACCGCCGCTCACTAGTGCGAGCGCGATCCGTGCCACCTCCGGTACTGCTGCCCCACCTCGCCAGCTGGTTGGAAGGC[A/G]
TCAATGGTGCTAGTGACCTCCCCCTCCCACCCCCCATCCCCCTTCGTCGGCTCTTCATTGAAGTTTGGGTTGTCACCTCCCCGCTAGAAAAAAAGAGGAG

Reverse complement sequence

CTCCTCTTTTTTTCTAGCGGGGAGGTGACAACCCAAACTTCAATGAAGAGCCGACGAAGGGGGATGGGGGGTGGGAGGGGGAGGTCACTAGCACCATTGA[T/C]
GCCTTCCAACCAGCTGGCGAGGTGGGGCAGCAGTACCGGAGGTGGCACGGATCGCGCTCGCACTAGTGAGCGGCGGTGGCATGAGGGGAGTCGGGAGAAA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	74.20%	25.50%	0.25%	0.00%	NA
All Indica	2759	67.20%	32.50%	0.36%	0.00%	NA
All Japonica	1512	99.50%	0.50%	0.00%	0.00%	NA
Aus	269	2.20%	97.80%	0.00%	0.00%	NA
Indica I	595	90.80%	8.90%	0.34%	0.00%	NA
Indica II	465	40.00%	59.10%	0.86%	0.00%	NA
Indica III	913	65.60%	34.40%	0.00%	0.00%	NA
Indica Intermediate	786	67.20%	32.30%	0.51%	0.00%	NA
Temperate Japonica	767	99.70%	0.30%	0.00%	0.00%	NA
Tropical Japonica	504	99.40%	0.60%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	85.40%	14.60%	0.00%	0.00%	NA
Intermediate	90	70.00%	27.80%	2.22%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0328953433	A -> G	LOC_Os03g50710.1	upstream_gene_variant ; 909.0bp to feature; MODIFIER	silent_mutation	Average:74.677; most accessible tissue: Callus, score: 96.443	N	N	N	N
vg0328953433	A -> G	LOC_Os03g50720.1	upstream_gene_variant ; 3963.0bp to feature; MODIFIER	silent_mutation	Average:74.677; most accessible tissue: Callus, score: 96.443	N	N	N	N
vg0328953433	A -> G	LOC_Os03g50690-LOC_Os03g50710	intergenic_region ; MODIFIER	silent_mutation	Average:74.677; most accessible tissue: Callus, score: 96.443	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0328953433	NA	2.91E-07	Grain_thickness	Ind_All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0328953433	8.92E-07	NA	mr1003	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0328953433	9.35E-07	1.54E-08	mr1003	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0328953433	NA	3.04E-06	mr1010	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0328953433	1.03E-06	NA	mr1051	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0328953433	3.12E-07	6.43E-09	mr1051	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
vg0328953433	NA	5.72E-06	mr1163	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0328953433	NA	4.94E-09	mr1193	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0328953433	6.41E-06	2.86E-07	mr1536	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0328953433	NA	7.12E-06	mr1657	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0328953433	NA	4.96E-06	mr1745	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0328953433	8.36E-06	8.35E-06	mr1832	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0328953433	NA	7.96E-07	mr1931	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0328953433	NA	2.07E-06	mr1974	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0328953433	NA	9.10E-11	mr1193_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0328953433	NA	1.83E-06	mr1952_2	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251