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Detailed information for vg0906460381:

Variant ID: vg0906460381 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 6460381
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:

ATGTCCGCACAATCTTGTCGGCATCGGACACAGCGGTGGGCCAGAAAAAACCTTGCCGGTACGCCTTGCTGACTATGGTGCGTGCAGCAGCATGGTTGCC[A/G]
CAAATACCAGAATGTATGTCCTTCAGCAATTGTCTCCCTTCTTCTAAGGATACACAGCGTTGCAGAATTCCTGATGGACTTTTCCTGTACAGCTCGGTCT

Reverse complement sequence

AGACCGAGCTGTACAGGAAAAGTCCATCAGGAATTCTGCAACGCTGTGTATCCTTAGAAGAAGGGAGACAATTGCTGAAGGACATACATTCTGGTATTTG[T/C]
GGCAACCATGCTGCTGCACGCACCATAGTCAGCAAGGCGTACCGGCAAGGTTTTTTCTGGCCCACCGCTGTGTCCGATGCCGACAAGATTGTGCGGACAT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	81.90%	0.60%	1.33%	16.21%	NA
All Indica	2759	72.90%	0.80%	2.07%	24.21%	NA
All Japonica	1512	99.60%	0.00%	0.00%	0.40%	NA
Aus	269	79.90%	0.70%	0.74%	18.59%	NA
Indica I	595	97.30%	0.00%	0.17%	2.52%	NA
Indica II	465	58.10%	0.60%	4.09%	37.20%	NA
Indica III	913	65.70%	1.40%	2.63%	30.23%	NA
Indica Intermediate	786	71.60%	0.80%	1.65%	25.95%	NA
Temperate Japonica	767	99.70%	0.00%	0.00%	0.26%	NA
Tropical Japonica	504	99.60%	0.00%	0.00%	0.40%	NA
Japonica Intermediate	241	99.20%	0.00%	0.00%	0.83%	NA
VI/Aromatic	96	63.50%	1.00%	4.17%	31.25%	NA
Intermediate	90	85.60%	1.10%	0.00%	13.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0906460381	A -> G	LOC_Os09g11560.1	downstream_gene_variant ; 4987.0bp to feature; MODIFIER	silent_mutation	Average:41.034; most accessible tissue: Minghui63 young leaf, score: 65.92	N	N	N	N
vg0906460381	A -> G	LOC_Os09g11570.1	downstream_gene_variant ; 1939.0bp to feature; MODIFIER	silent_mutation	Average:41.034; most accessible tissue: Minghui63 young leaf, score: 65.92	N	N	N	N
vg0906460381	A -> G	LOC_Os09g11580.1	intron_variant ; MODIFIER	silent_mutation	Average:41.034; most accessible tissue: Minghui63 young leaf, score: 65.92	N	N	N	N
vg0906460381	A -> DEL	N	N	silent_mutation	Average:41.034; most accessible tissue: Minghui63 young leaf, score: 65.92	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0906460381	2.55E-06	1.77E-06	mr1133_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
vg0906460381	9.18E-06	9.18E-06	mr1912_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