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Detailed information for vg1005306011:

Variant ID: vg1005306011 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 5306011
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.93, A: 0.08, others allele: 0.00, population size: 113. )

Flanking Sequence (100 bp) in Reference Genome:

ATTCTAGTTTGTGAATTTCTGGGCGTGACATACCTCCCCCACTTCATCTTGCATAGTTGTCGGTAATGATTCCCTCCTTCCTATCACTGCAACTGGTAGC[A/G]
CTCGAATCAATTACCCACACAATTCCTTTCTTCTTAATAATGTCCTTGTTTCTCCTGCCATTATTAAAAGCCTTATATCTGCTCGCCGTTTTACTCGTGG

Reverse complement sequence

CCACGAGTAAAACGGCGAGCAGATATAAGGCTTTTAATAATGGCAGGAGAAACAAGGACATTATTAAGAAGAAAGGAATTGTGTGGGTAATTGATTCGAG[T/C]
GCTACCAGTTGCAGTGATAGGAAGGAGGGAATCATTACCGACAACTATGCAAGATGAAGTGGGGGAGGTATGTCACGCCCAGAAATTCACAAACTAGAAT

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	51.80%	39.40%	0.53%	8.27%	NA
All Indica	2759	45.70%	49.10%	0.65%	4.53%	NA
All Japonica	1512	71.60%	13.20%	0.26%	15.01%	NA
Aus	269	1.90%	98.10%	0.00%	0.00%	NA
Indica I	595	60.00%	39.50%	0.50%	0.00%	NA
Indica II	465	41.10%	48.00%	1.08%	9.89%	NA
Indica III	913	44.10%	49.00%	0.55%	6.35%	NA
Indica Intermediate	786	39.60%	57.10%	0.64%	2.67%	NA
Temperate Japonica	767	74.10%	16.30%	0.13%	9.52%	NA
Tropical Japonica	504	71.40%	9.50%	0.60%	18.45%	NA
Japonica Intermediate	241	63.90%	10.80%	0.00%	25.31%	NA
VI/Aromatic	96	42.70%	27.10%	1.04%	29.17%	NA
Intermediate	90	62.20%	23.30%	2.22%	12.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1005306011	A -> G	LOC_Os10g09800.1	downstream_gene_variant ; 3824.0bp to feature; MODIFIER	silent_mutation	Average:34.625; most accessible tissue: Zhenshan97 panicle, score: 61.671	N	N	N	N
vg1005306011	A -> G	LOC_Os10g09810.1	intron_variant ; MODIFIER	silent_mutation	Average:34.625; most accessible tissue: Zhenshan97 panicle, score: 61.671	N	N	N	N
vg1005306011	A -> DEL	N	N	silent_mutation	Average:34.625; most accessible tissue: Zhenshan97 panicle, score: 61.671	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1005306011	NA	2.71E-06	mr1207	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
vg1005306011	NA	1.35E-07	mr1286	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
vg1005306011	NA	3.08E-07	mr1420	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
vg1005306011	NA	7.95E-08	mr1556	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
vg1005306011	NA	2.30E-06	mr1569	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
vg1005306011	NA	3.53E-06	mr1574	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
vg1005306011	NA	3.02E-07	mr1659	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
vg1005306011	NA	4.75E-09	mr1665	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
vg1005306011	NA	5.00E-06	mr1687	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
vg1005306011	NA	4.38E-07	mr1764	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
vg1005306011	3.40E-06	3.04E-07	mr1976	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