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Detailed information for vg0729357717:

Variant ID: vg0729357717 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 29357717
Reference Allele: G	Alternative Allele: T
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, T: 0.01, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:

AGATGACGCCGTTAACTTTTTCTCACATGTTTAACCATTCGTTTTATTCAAAAATTTTATGCAATTGTATAAGATATAAATCACACTTAAAATACTATGA[G/T]
TAATAAAACAACTCATAACAAAATAAATTATAATTACCTAAATTTTTTAAATAAGACGAATGGTCAAACATGTGAGAAAAAGTTAACGGCGTTATCTATT

Reverse complement sequence

AATAGATAACGCCGTTAACTTTTTCTCACATGTTTGACCATTCGTCTTATTTAAAAAATTTAGGTAATTATAATTTATTTTGTTATGAGTTGTTTTATTA[C/A]
TCATAGTATTTTAAGTGTGATTTATATCTTATACAATTGCATAAAATTTTTGAATAAAACGAATGGTTAAACATGTGAGAAAAAGTTAACGGCGTCATCT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	58.70%	41.20%	0.11%	0.00%	NA
All Indica	2759	90.10%	9.70%	0.11%	0.00%	NA
All Japonica	1512	6.70%	93.30%	0.00%	0.00%	NA
Aus	269	54.60%	45.00%	0.37%	0.00%	NA
Indica I	595	99.20%	0.80%	0.00%	0.00%	NA
Indica II	465	92.70%	7.10%	0.22%	0.00%	NA
Indica III	913	84.60%	15.30%	0.11%	0.00%	NA
Indica Intermediate	786	88.30%	11.60%	0.13%	0.00%	NA
Temperate Japonica	767	0.80%	99.20%	0.00%	0.00%	NA
Tropical Japonica	504	5.40%	94.60%	0.00%	0.00%	NA
Japonica Intermediate	241	28.60%	71.40%	0.00%	0.00%	NA
VI/Aromatic	96	3.10%	96.90%	0.00%	0.00%	NA
Intermediate	90	37.80%	61.10%	1.11%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0729357717	G -> T	LOC_Os07g49030.1	upstream_gene_variant ; 402.0bp to feature; MODIFIER	silent_mutation	Average:89.253; most accessible tissue: Callus, score: 94.482	N	N	N	N
vg0729357717	G -> T	LOC_Os07g49030.2	upstream_gene_variant ; 800.0bp to feature; MODIFIER	silent_mutation	Average:89.253; most accessible tissue: Callus, score: 94.482	N	N	N	N
vg0729357717	G -> T	LOC_Os07g49030-LOC_Os07g49040	intergenic_region ; MODIFIER	silent_mutation	Average:89.253; most accessible tissue: Callus, score: 94.482	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0729357717	9.80E-06	9.80E-06	mr1008	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
vg0729357717	5.24E-06	5.24E-06	mr1009	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
vg0729357717	NA	7.84E-06	mr1208	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
vg0729357717	NA	1.00E-09	mr1342	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
vg0729357717	NA	7.71E-07	mr1693	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
vg0729357717	NA	2.69E-07	mr1212_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
vg0729357717	NA	5.79E-08	mr1299_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
vg0729357717	NA	4.83E-17	mr1592_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
vg0729357717	NA	2.40E-10	mr1595_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
vg0729357717	NA	1.54E-09	mr1600_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
vg0729357717	NA	3.06E-07	mr1691_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
vg0729357717	NA	9.25E-09	mr1700_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
vg0729357717	NA	5.42E-07	mr1720_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
vg0729357717	NA	1.07E-06	mr1727_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
vg0729357717	NA	4.70E-06	mr1785_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
vg0729357717	NA	1.65E-07	mr1804_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
vg0729357717	NA	2.82E-08	mr1837_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
vg0729357717	4.11E-06	4.96E-37	mr1888_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
vg0729357717	NA	3.28E-14	mr1938_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