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Detailed information for vg0321139464:

Variant ID: vg0321139464 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 21139464
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:

TTGTGAACCACTGGGTCTAGTACCAGGGGGTACCGCCCCGGGTGGACCACTCGGTTAGGATGATCCGAGCGGTCAAACTTAATTGTTGTCTCTGACCATC[G/A]
AAGATATTGGGGCGTGTTGGGCTGAACAACATTGATCTCTCGTTCGGTCAGCTTTTGCTTTCTCTTGGATTCATAAGCTAGGGGTCCGCCAAAGATGTGG

Reverse complement sequence

CCACATCTTTGGCGGACCCCTAGCTTATGAATCCAAGAGAAAGCAAAAGCTGACCGAACGAGAGATCAATGTTGTTCAGCCCAACACGCCCCAATATCTT[C/T]
GATGGTCAGAGACAACAATTAAGTTTGACCGCTCGGATCATCCTAACCGAGTGGTCCACCCGGGGCGGTACCCCCTGGTACTAGACCCAGTGGTTCACAA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	55.30%	44.40%	0.25%	0.00%	NA
All Indica	2759	25.90%	73.80%	0.33%	0.00%	NA
All Japonica	1512	97.90%	1.90%	0.20%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	75.30%	24.40%	0.34%	0.00%	NA
Indica II	465	7.50%	91.80%	0.65%	0.00%	NA
Indica III	913	7.00%	93.00%	0.00%	0.00%	NA
Indica Intermediate	786	21.20%	78.20%	0.51%	0.00%	NA
Temperate Japonica	767	99.60%	0.40%	0.00%	0.00%	NA
Tropical Japonica	504	94.80%	4.80%	0.40%	0.00%	NA
Japonica Intermediate	241	99.20%	0.40%	0.41%	0.00%	NA
VI/Aromatic	96	96.90%	3.10%	0.00%	0.00%	NA
Intermediate	90	65.60%	34.40%	0.00%	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
vg0321139464	G -> A	LOC_Os03g38082.1	stop_gained ; p.Arg428*; HIGH	stop_gained	Average:50.706; most accessible tissue: Minghui63 young leaf, score: 70.038	N	N	N	N
vg0321139464	G -> A	LOC_Os03g38082.1	stop_gained ; p.Arg428*; HIGH	nonsynonymous_codon ; R428W	Average:50.706; most accessible tissue: Minghui63 young leaf, score: 70.038	benign	0.875	DELETERIOUS	0.02

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0321139464	NA	6.99E-15	Grain_length	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
vg0321139464	NA	1.39E-14	Grain_length	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
vg0321139464	NA	2.37E-06	Spikelet_length	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
vg0321139464	NA	2.94E-06	mr1030	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
vg0321139464	NA	1.97E-06	mr1046	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
vg0321139464	NA	1.77E-07	mr1058	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
vg0321139464	NA	1.49E-06	mr1221	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
vg0321139464	NA	6.40E-07	mr1568	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
vg0321139464	NA	4.51E-06	mr1621	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
vg0321139464	NA	2.44E-11	mr1637	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
vg0321139464	NA	2.59E-09	mr1663	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
vg0321139464	NA	2.59E-09	mr1669	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
vg0321139464	NA	5.27E-07	mr1785	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
vg0321139464	NA	8.72E-10	mr1804	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
vg0321139464	NA	2.72E-07	mr1928	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
vg0321139464	NA	1.91E-09	mr1108_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
vg0321139464	NA	1.82E-11	mr1188_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
vg0321139464	NA	1.57E-10	mr1565_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
vg0321139464	3.30E-06	NA	mr1750_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