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Detailed information for vg0818631289:

Variant ID: vg0818631289 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 18631289
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, A: 0.00, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:

TCTGACCGATTGGACAATGTCGGTCTAACCGTGCTCCTCGAATTAAAACCCGATTTTTGCCAACGTCGTTTTGCAAAAGCAATTTCTCTTTCCTTTTTCT[G/A]
TTTATGGGCAAGTCAAACAAAAACCAACTAAATGTCCATCTTTTCCGCAAAAAGAACAAGTGTACTTTTCACGACAAGTTTGTGAAGTAGATTGTTTTGA

Reverse complement sequence

TCAAAACAATCTACTTCACAAACTTGTCGTGAAAAGTACACTTGTTCTTTTTGCGGAAAAGATGGACATTTAGTTGGTTTTTGTTTGACTTGCCCATAAA[C/T]
AGAAAAAGGAAAGAGAAATTGCTTTTGCAAAACGACGTTGGCAAAAATCGGGTTTTAATTCGAGGAGCACGGTTAGACCGACATTGTCCAATCGGTCAGA

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	84.00%	10.30%	4.91%	0.76%	NA
All Indica	2759	83.00%	10.10%	6.92%	0.00%	NA
All Japonica	1512	81.90%	13.40%	2.25%	2.38%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	96.60%	1.00%	2.35%	0.00%	NA
Indica II	465	94.60%	2.40%	3.01%	0.00%	NA
Indica III	913	72.10%	18.60%	9.31%	0.00%	NA
Indica Intermediate	786	78.40%	11.70%	9.92%	0.00%	NA
Temperate Japonica	767	91.30%	0.00%	4.04%	4.69%	NA
Tropical Japonica	504	63.50%	36.30%	0.20%	0.00%	NA
Japonica Intermediate	241	90.90%	8.30%	0.83%	0.00%	NA
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	88.90%	4.40%	6.67%	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
vg0818631289	G -> A	LOC_Os08g30280.1	splice_region_variant&intron_variant ; LOW	silent_mutation	Average:35.445; most accessible tissue: Minghui63 young leaf, score: 49.581	N	N	N	N
vg0818631289	G -> A	LOC_Os08g30290.1	downstream_gene_variant ; 1637.0bp to feature; MODIFIER	silent_mutation	Average:35.445; most accessible tissue: Minghui63 young leaf, score: 49.581	N	N	N	N
vg0818631289	G -> DEL	N	N	silent_mutation	Average:35.445; most accessible tissue: Minghui63 young leaf, score: 49.581	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0818631289	NA	6.87E-06	mr1073	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
vg0818631289	7.00E-08	7.00E-08	mr1266	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
vg0818631289	1.66E-06	2.65E-07	mr1345	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
vg0818631289	NA	1.71E-06	mr1345	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
vg0818631289	NA	9.87E-06	mr1382	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
vg0818631289	1.79E-06	1.80E-06	mr1511	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
vg0818631289	NA	5.62E-06	mr1700	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
vg0818631289	NA	2.75E-08	mr1830	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
vg0818631289	NA	8.73E-09	mr1047_2	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
vg0818631289	NA	5.03E-06	mr1870_2	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