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Detailed information for vg0905314628:

Variant ID: vg0905314628 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 5314628
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 222. )

Flanking Sequence (100 bp) in Reference Genome:

AGTGCTTCCGATCCAGTCGGCCAGTCAGATGCTCGCAAGAGGAAGCTGGTTCTAAGCGACGAGGAAGGCGATGATACCGGAAGGCTCGGAGAAAAAGGAG[C/T]
GACCGGAAAATCCCCAAAGCCAACTAATCCGAAGAAGAAAACCTCCAGTCGTCCTTTGCCAAAAATCAGAAAGTCTTCCAGGTACAAACCATTTGGCCAT

Reverse complement sequence

ATGGCCAAATGGTTTGTACCTGGAAGACTTTCTGATTTTTGGCAAAGGACGACTGGAGGTTTTCTTCTTCGGATTAGTTGGCTTTGGGGATTTTCCGGTC[G/A]
CTCCTTTTTCTCCGAGCCTTCCGGTATCATCGCCTTCCTCGTCGCTTAGAACCAGCTTCCTCTTGCGAGCATCTGACTGGCCGACTGGATCGGAAGCACT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	69.60%	13.80%	16.63%	0.00%	NA
All Indica	2759	50.30%	22.70%	27.00%	0.00%	NA
All Japonica	1512	99.20%	0.30%	0.53%	0.00%	NA
Aus	269	89.60%	4.10%	6.32%	0.00%	NA
Indica I	595	51.80%	9.20%	38.99%	0.00%	NA
Indica II	465	31.40%	28.40%	40.22%	0.00%	NA
Indica III	913	56.50%	32.10%	11.39%	0.00%	NA
Indica Intermediate	786	53.10%	18.70%	28.24%	0.00%	NA
Temperate Japonica	767	99.50%	0.00%	0.52%	0.00%	NA
Tropical Japonica	504	98.80%	0.60%	0.60%	0.00%	NA
Japonica Intermediate	241	99.20%	0.40%	0.41%	0.00%	NA
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	72.20%	11.10%	16.67%	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
vg0905314628	C -> T	LOC_Os09g09800.1	missense_variant ; p.Ala365Val; MODERATE	nonsynonymous_codon ; A365V	Average:17.759; most accessible tissue: Minghui63 panicle, score: 20.733	unknown	unknown	TOLERATED	0.71

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0905314628	NA	1.30E-06	mr1386	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
vg0905314628	NA	8.61E-07	mr1414	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
vg0905314628	NA	1.71E-08	mr1622	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
vg0905314628	NA	7.19E-06	mr1622	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
vg0905314628	NA	4.17E-08	mr1830	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
vg0905314628	NA	1.78E-09	mr1846	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
vg0905314628	NA	4.48E-06	mr1304_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
vg0905314628	NA	1.57E-06	mr1608_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
vg0905314628	NA	5.18E-16	mr1830_2	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
vg0905314628	NA	1.04E-11	mr1830_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
vg0905314628	6.99E-07	5.70E-22	mr1846_2	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
vg0905314628	5.13E-06	2.45E-22	mr1846_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