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Detailed information for vg0906547680:

Variant ID: vg0906547680 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 6547680
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.98, A: 0.03, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:

CCTCCGTTCCAAAATAAATCAACTTATAGAATTCAAACTTTGTCCTAAAATAAATCAACTTCTATCTTCTTATTCACTGTTGATTCGCAAATCAAAAAAA[T/A]
TTATTCCTTCAATACCCCTTGCCTACATATCTACCAATACTAGCTATTAATATATGCAGGTAGTTTTCAGGGCAACACATTGACTCCGGTCTTGGGCACA

Reverse complement sequence

TGTGCCCAAGACCGGAGTCAATGTGTTGCCCTGAAAACTACCTGCATATATTAATAGCTAGTATTGGTAGATATGTAGGCAAGGGGTATTGAAGGAATAA[A/T]
TTTTTTTGATTTGCGAATCAACAGTGAATAAGAAGATAGAAGTTGATTTATTTTAGGACAAAGTTTGAATTCTATAAGTTGATTTATTTTGGAACGGAGG

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	66.20%	31.80%	0.28%	1.69%	NA
All Indica	2759	48.50%	50.10%	0.40%	1.05%	NA
All Japonica	1512	98.50%	0.50%	0.07%	0.93%	NA
Aus	269	51.30%	35.30%	0.00%	13.38%	NA
Indica I	595	29.60%	70.30%	0.17%	0.00%	NA
Indica II	465	63.40%	30.50%	1.29%	4.73%	NA
Indica III	913	48.50%	51.50%	0.00%	0.00%	NA
Indica Intermediate	786	53.90%	44.70%	0.51%	0.89%	NA
Temperate Japonica	767	99.20%	0.70%	0.00%	0.13%	NA
Tropical Japonica	504	96.80%	0.40%	0.20%	2.58%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	95.80%	4.20%	0.00%	0.00%	NA
Intermediate	90	81.10%	16.70%	1.11%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0906547680	T -> DEL	N	N	silent_mutation	Average:47.699; most accessible tissue: Zhenshan97 young leaf, score: 74.302	N	N	N	N
vg0906547680	T -> A	LOC_Os09g11730.1	intron_variant ; MODIFIER	silent_mutation	Average:47.699; most accessible tissue: Zhenshan97 young leaf, score: 74.302	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0906547680	NA	4.22E-06	mr1201	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
vg0906547680	NA	2.43E-06	mr1137_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
vg0906547680	6.13E-08	8.66E-07	mr1160_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
vg0906547680	NA	2.12E-06	mr1160_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
vg0906547680	NA	6.57E-07	mr1201_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
vg0906547680	NA	1.79E-06	mr1219_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
vg0906547680	NA	5.56E-06	mr1617_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