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Detailed information for vg0102429074:

Variant ID: vg0102429074 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 2429074
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.81, T: 0.19, others allele: 0.00, population size: 68. )

Flanking Sequence (100 bp) in Reference Genome:

TATTTATTCTTTTCATATCATTTGATTCATTGTTAAATATACTTTCATGTGCACATATAGTTTTACATATTTCACAATTTTTTTTAATAAGACGAATAGT[C/T]
AAATATGTGCTAAAAAGTCAATGGTGTCAAACATTTTGAAACGGAGGGAGTATTTGAGGATACGCCCTCGTGAAAATGAAAGAAAAAGGAGAGATAGAGA

Reverse complement sequence

TCTCTATCTCTCCTTTTTCTTTCATTTTCACGAGGGCGTATCCTCAAATACTCCCTCCGTTTCAAAATGTTTGACACCATTGACTTTTTAGCACATATTT[G/A]
ACTATTCGTCTTATTAAAAAAAATTGTGAAATATGTAAAACTATATGTGCACATGAAAGTATATTTAACAATGAATCAAATGATATGAAAAGAATAAATA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	44.70%	18.50%	0.25%	36.50%	NA
All Indica	2759	53.90%	11.30%	0.33%	34.43%	NA
All Japonica	1512	35.40%	23.30%	0.13%	41.20%	NA
Aus	269	13.40%	58.40%	0.00%	28.25%	NA
Indica I	595	28.60%	7.10%	0.84%	63.53%	NA
Indica II	465	87.30%	6.50%	0.00%	6.24%	NA
Indica III	913	51.60%	15.10%	0.11%	33.19%	NA
Indica Intermediate	786	56.00%	13.10%	0.38%	30.53%	NA
Temperate Japonica	767	18.40%	37.30%	0.13%	44.20%	NA
Tropical Japonica	504	66.90%	5.40%	0.20%	27.58%	NA
Japonica Intermediate	241	23.70%	16.20%	0.00%	60.17%	NA
VI/Aromatic	96	11.50%	34.40%	0.00%	54.17%	NA
Intermediate	90	48.90%	23.30%	1.11%	26.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0102429074	C -> T	LOC_Os01g05170-LOC_Os01g05180	intergenic_region ; MODIFIER	silent_mutation	Average:39.288; most accessible tissue: Minghui63 root, score: 68.289	N	N	N	N
vg0102429074	C -> DEL	N	N	silent_mutation	Average:39.288; most accessible tissue: Minghui63 root, score: 68.289	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0102429074	NA	5.31E-06	mr1598	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
vg0102429074	NA	7.80E-12	mr1769	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
vg0102429074	NA	9.16E-08	mr1125_2	Jap_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
vg0102429074	NA	7.46E-08	mr1347_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
vg0102429074	NA	8.87E-06	mr1406_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
vg0102429074	NA	2.75E-06	mr1553_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
vg0102429074	NA	8.38E-06	mr1623_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
vg0102429074	NA	8.15E-11	mr1769_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
vg0102429074	NA	1.45E-06	mr1970_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