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Detailed information for vg0900634520:

Variant ID: vg0900634520 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 634520
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, T: 0.04, others allele: 0.00, population size: 227. )

Flanking Sequence (100 bp) in Reference Genome:

ATAGACATCGTTGACATTCACATAGGATTGAAATCATATGGATAACATTGTGAACATGTAAATAACAAGAAGAAAATCAAATAAAGTTAGAATCTTATAC[C/T]
CAGAGAATAGTGCAGAAGATGTTGAGTCATTCGTATTGCCTCCGTTGATGTTGTCTCCTCCGTTCTCTCCAGTAGAAGCCATGGTGAAGCGGAAGTAGAG

Reverse complement sequence

CTCTACTTCCGCTTCACCATGGCTTCTACTGGAGAGAACGGAGGAGACAACATCAACGGAGGCAATACGAATGACTCAACATCTTCTGCACTATTCTCTG[G/A]
GTATAAGATTCTAACTTTATTTGATTTTCTTCTTGTTATTTACATGTTCACAATGTTATCCATATGATTTCAATCCTATGTGAATGTCAACGATGTCTAT

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	66.50%	33.10%	0.36%	0.04%	NA
All Indica	2759	52.80%	46.60%	0.58%	0.07%	NA
All Japonica	1512	99.50%	0.50%	0.00%	0.00%	NA
Aus	269	3.00%	97.00%	0.00%	0.00%	NA
Indica I	595	61.30%	38.50%	0.17%	0.00%	NA
Indica II	465	72.00%	27.50%	0.22%	0.22%	NA
Indica III	913	41.80%	57.10%	0.99%	0.11%	NA
Indica Intermediate	786	47.60%	51.80%	0.64%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	99.00%	1.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	87.80%	11.10%	1.11%	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
vg0900634520	C -> DEL	N	N	silent_mutation	Average:60.628; most accessible tissue: Zhenshan97 panicle, score: 75.67	N	N	N	N
vg0900634520	C -> T	LOC_Os09g01950.1	downstream_gene_variant ; 3222.0bp to feature; MODIFIER	silent_mutation	Average:60.628; most accessible tissue: Zhenshan97 panicle, score: 75.67	N	N	N	N
vg0900634520	C -> T	LOC_Os09g01940-LOC_Os09g01950	intergenic_region ; MODIFIER	silent_mutation	Average:60.628; most accessible tissue: Zhenshan97 panicle, score: 75.67	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0900634520	NA	3.66E-06	mr1066	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
vg0900634520	NA	6.22E-06	mr1104	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
vg0900634520	NA	3.62E-07	mr1155	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
vg0900634520	4.81E-06	4.99E-07	mr1408	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