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Detailed information for vg0909260803:

Variant ID: vg0909260803 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 9260803
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

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

Flanking Sequence (100 bp) in Reference Genome:

AATTTTACGACCATATTACATGGGGCTATATACCTCATACCAAAATTTTGTTTGTTTTGTGCAACTTTAACTATAACAGATAGGGTTTCATGAAATTTAC[C/T]
CATTATTTTTCACGAACAAGGACTAACATTTTGTTGCTTGGCTATTAGCATAATTGGCTTAACAAGTGGCTTGAGAGCTAGTAGGATGGATCCATTATAC

Reverse complement sequence

GTATAATGGATCCATCCTACTAGCTCTCAAGCCACTTGTTAAGCCAATTATGCTAATAGCCAAGCAACAAAATGTTAGTCCTTGTTCGTGAAAAATAATG[G/A]
GTAAATTTCATGAAACCCTATCTGTTATAGTTAAAGTTGCACAAAACAAACAAAATTTTGGTATGAGGTATATAGCCCCATGTAATATGGTCGTAAAATT

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	71.60%	28.40%	0.08%	0.00%	NA
All Indica	2759	94.70%	5.30%	0.00%	0.00%	NA
All Japonica	1512	24.50%	75.40%	0.13%	0.00%	NA
Aus	269	98.10%	1.90%	0.00%	0.00%	NA
Indica I	595	94.50%	5.50%	0.00%	0.00%	NA
Indica II	465	98.90%	1.10%	0.00%	0.00%	NA
Indica III	913	91.20%	8.80%	0.00%	0.00%	NA
Indica Intermediate	786	96.30%	3.70%	0.00%	0.00%	NA
Temperate Japonica	767	17.30%	82.50%	0.13%	0.00%	NA
Tropical Japonica	504	28.00%	72.00%	0.00%	0.00%	NA
Japonica Intermediate	241	39.80%	59.80%	0.41%	0.00%	NA
VI/Aromatic	96	82.30%	17.70%	0.00%	0.00%	NA
Intermediate	90	63.30%	34.40%	2.22%	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
vg0909260803	C -> T	LOC_Os09g15250.1	upstream_gene_variant ; 3403.0bp to feature; MODIFIER	silent_mutation	Average:36.974; most accessible tissue: Zhenshan97 panicle, score: 52.263	N	N	N	N
vg0909260803	C -> T	LOC_Os09g15240-LOC_Os09g15250	intergenic_region ; MODIFIER	silent_mutation	Average:36.974; most accessible tissue: Zhenshan97 panicle, score: 52.263	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0909260803	NA	3.01E-34	mr1137_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
vg0909260803	NA	6.92E-06	mr1318_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
vg0909260803	NA	1.09E-11	mr1377_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
vg0909260803	NA	1.77E-32	mr1617_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
vg0909260803	NA	3.01E-06	mr1617_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
vg0909260803	NA	1.15E-18	mr1637_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
vg0909260803	NA	1.54E-06	mr1702_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
vg0909260803	NA	2.46E-11	mr1705_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
vg0909260803	NA	1.35E-13	mr1713_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
vg0909260803	NA	5.67E-07	mr1727_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
vg0909260803	NA	9.20E-09	mr1741_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
vg0909260803	NA	3.55E-08	mr1783_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
vg0909260803	NA	3.52E-07	mr1785_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
vg0909260803	NA	4.87E-08	mr1804_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