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Detailed information for vg0906561460:

Variant ID: vg0906561460 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 6561460
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.68, A: 0.32, others allele: 0.00, population size: 168. )

Flanking Sequence (100 bp) in Reference Genome:

ATCTAAAAGGGCAGTAGTTTGGACATCAGCCAAGAGAACATTGTACTCATCCAAAGCCTGTTGAGACAATGGCAAGAAGAATTGATCTTGAGGTTCTCTC[G/A]
CCAAGTGCTGAGAAACAGAGTCTTCCTTGTGTCTTGCAAACGAGAACAGCCTTGGGAATTTGACAGATCTTACCATACCATTCCATAGATCATCCTAAGA

Reverse complement sequence

TCTTAGGATGATCTATGGAATGGTATGGTAAGATCTGTCAAATTCCCAAGGCTGTTCTCGTTTGCAAGACACAAGGAAGACTCTGTTTCTCAGCACTTGG[C/T]
GAGAGAACCTCAAGATCAATTCTTCTTGCCATTGTCTCAACAGGCTTTGGATGAGTACAATGTTCTCTTGGCTGATGTCCAAACTACTGCCCTTTTAGAT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	42.90%	35.30%	0.49%	21.31%	NA
All Indica	2759	16.40%	52.60%	0.69%	30.34%	NA
All Japonica	1512	98.10%	1.40%	0.00%	0.53%	NA
Aus	269	10.80%	49.80%	1.12%	38.29%	NA
Indica I	595	24.90%	71.10%	0.00%	4.03%	NA
Indica II	465	8.40%	38.30%	1.51%	51.83%	NA
Indica III	913	12.40%	52.20%	0.55%	34.83%	NA
Indica Intermediate	786	19.50%	47.30%	0.89%	32.32%	NA
Temperate Japonica	767	99.30%	0.10%	0.00%	0.52%	NA
Tropical Japonica	504	99.00%	0.60%	0.00%	0.40%	NA
Japonica Intermediate	241	92.10%	7.10%	0.00%	0.83%	NA
VI/Aromatic	96	15.60%	40.60%	0.00%	43.75%	NA
Intermediate	90	52.20%	27.80%	1.11%	18.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0906561460	G -> DEL	LOC_Os09g11740.1	N	frameshift_variant	Average:44.172; most accessible tissue: Zhenshan97 young leaf, score: 77.422	N	N	N	N
vg0906561460	G -> A	LOC_Os09g11740.1	missense_variant ; p.Ala153Val; MODERATE	nonsynonymous_codon ; A153V	Average:44.172; most accessible tissue: Zhenshan97 young leaf, score: 77.422	unknown	unknown	TOLERATED	0.14

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0906561460	8.13E-06	3.08E-14	mr1188_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
vg0906561460	2.12E-06	9.04E-10	mr1188_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
vg0906561460	NA	7.28E-06	mr1354_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
vg0906561460	NA	7.12E-06	mr1931_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