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Detailed information for vg0410214235:

Variant ID: vg0410214235 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 10214235
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.95, G: 0.05, others allele: 0.00, population size: 62. )

Flanking Sequence (100 bp) in Reference Genome:

GCAAGGTGACAAGATTGAGATCGTGCCAGCCGACAGGTCAGTTAATGTTGCCAGTGCCGATTTAGCTCTTTGGGAGATGGACGGTATTGATTGCTTGTCT[A/G]
GAAAGTGTCCGATTGTGATATACAACCGATTGAAGATGGAGAGCCCAAGTTATTATTTTGAGGGCGTCGTGGAGGGTTCAAACGTCTACACCAAGGACAC

Reverse complement sequence

GTGTCCTTGGTGTAGACGTTTGAACCCTCCACGACGCCCTCAAAATAATAACTTGGGCTCTCCATCTTCAATCGGTTGTATATCACAATCGGACACTTTC[T/C]
AGACAAGCAATCAATACCGTCCATCTCCCAAAGAGCTAAATCGGCACTGGCAACATTAACTGACCTGTCGGCTGGCACGATCTCAATCTTGTCACCTTGC

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	36.40%	15.70%	5.67%	42.23%	NA
All Indica	2759	25.80%	1.70%	8.19%	64.30%	NA
All Japonica	1512	60.80%	38.30%	0.60%	0.26%	NA
Aus	269	19.70%	0.70%	5.95%	73.61%	NA
Indica I	595	53.90%	1.20%	6.55%	38.32%	NA
Indica II	465	29.20%	2.20%	9.89%	58.71%	NA
Indica III	913	2.60%	1.20%	8.65%	87.51%	NA
Indica Intermediate	786	29.40%	2.40%	7.89%	60.31%	NA
Temperate Japonica	767	95.80%	3.70%	0.26%	0.26%	NA
Tropical Japonica	504	4.60%	94.80%	0.40%	0.20%	NA
Japonica Intermediate	241	67.20%	30.30%	2.07%	0.41%	NA
VI/Aromatic	96	7.30%	85.40%	7.29%	0.00%	NA
Intermediate	90	33.30%	33.30%	11.11%	22.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0410214235	A -> DEL	LOC_Os04g18480.1	N	frameshift_variant	Average:11.714; most accessible tissue: Callus, score: 19.156	N	N	N	N
vg0410214235	A -> G	LOC_Os04g18480.1	missense_variant ; p.Arg503Gly; MODERATE	nonsynonymous_codon ; R503G	Average:11.714; most accessible tissue: Callus, score: 19.156	unknown	unknown	TOLERATED	0.40

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0410214235	NA	3.24E-06	mr1045	Jap_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
vg0410214235	NA	2.42E-06	mr1081	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
vg0410214235	NA	9.30E-08	mr1194	Jap_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
vg0410214235	NA	1.27E-06	mr1388	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
vg0410214235	NA	1.12E-06	mr1403	Jap_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
vg0410214235	NA	1.69E-08	mr1449	Jap_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
vg0410214235	NA	2.73E-11	mr1454	Jap_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
vg0410214235	NA	5.29E-08	mr1552	Jap_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
vg0410214235	2.21E-06	2.21E-06	mr1556	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
vg0410214235	NA	5.27E-07	mr1715	Jap_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
vg0410214235	NA	4.19E-13	mr1789	Jap_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
vg0410214235	8.25E-07	6.02E-07	mr1797	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
vg0410214235	8.25E-07	6.02E-07	mr1801	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
vg0410214235	NA	1.33E-09	mr1880	Jap_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