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Detailed information for vg0606315830:

Variant ID: vg0606315830 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 6315830
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.56, T: 0.44, others allele: 0.00, population size: 32. )

Flanking Sequence (100 bp) in Reference Genome:

TTCCTCTAAAGTCCCACCCCTATATATATGTCTTCTTCCTCCTCCAGCTGCCCGAGCAAGCTTCAAAATTTCTTCAAAAAAGAGGGGAGGTCATGCCAAA[T/A]
TTTTTATTAAATTTATTTTGGTGATTACATACAAATCGGAGGTGCCTAAAAGGTTTGCAACTTCATCATCCAATGTTTTTTTTTCATACTACATTTGCAC

Reverse complement sequence

GTGCAAATGTAGTATGAAAAAAAAACATTGGATGATGAAGTTGCAAACCTTTTAGGCACCTCCGATTTGTATGTAATCACCAAAATAAATTTAATAAAAA[A/T]
TTTGGCATGACCTCCCCTCTTTTTTGAAGAAATTTTGAAGCTTGCTCGGGCAGCTGGAGGAGGAAGAAGACATATATATAGGGGTGGGACTTTAGAGGAA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	37.10%	3.20%	19.15%	40.54%	NA
All Indica	2759	19.00%	3.70%	20.30%	57.05%	NA
All Japonica	1512	77.50%	0.70%	2.12%	19.71%	NA
Aus	269	4.80%	7.40%	85.13%	2.60%	NA
Indica I	595	32.60%	2.20%	10.59%	54.62%	NA
Indica II	465	1.70%	4.50%	18.06%	75.70%	NA
Indica III	913	18.80%	3.30%	26.83%	51.04%	NA
Indica Intermediate	786	19.00%	4.80%	21.37%	54.83%	NA
Temperate Japonica	767	98.40%	0.30%	0.00%	1.30%	NA
Tropical Japonica	504	43.30%	1.00%	4.56%	51.19%	NA
Japonica Intermediate	241	82.60%	1.20%	3.73%	12.45%	NA
VI/Aromatic	96	7.30%	17.70%	69.79%	5.21%	NA
Intermediate	90	41.10%	4.40%	18.89%	35.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0606315830	T -> A	LOC_Os06g11880.1	upstream_gene_variant ; 464.0bp to feature; MODIFIER	silent_mutation	Average:9.18; most accessible tissue: Zhenshan97 root, score: 16.934	N	N	N	N
vg0606315830	T -> A	LOC_Os06g11870-LOC_Os06g11880	intergenic_region ; MODIFIER	silent_mutation	Average:9.18; most accessible tissue: Zhenshan97 root, score: 16.934	N	N	N	N
vg0606315830	T -> DEL	N	N	silent_mutation	Average:9.18; most accessible tissue: Zhenshan97 root, score: 16.934	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0606315830	NA	2.78E-06	mr1798	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
vg0606315830	NA	2.13E-06	mr1077_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
vg0606315830	NA	1.21E-07	mr1336_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
vg0606315830	2.37E-06	6.40E-09	mr1579_2	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
vg0606315830	NA	9.09E-08	mr1798_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
vg0606315830	NA	2.95E-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
vg0606315830	8.45E-06	8.45E-06	mr1877_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