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Detailed information for vg0406010273:

Variant ID: vg0406010273 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 6010273
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.67, T: 0.32, others allele: 0.00, population size: 191. )

Flanking Sequence (100 bp) in Reference Genome:

CCATCGAAAATCAGAAAATACATCATGTTAGGTTTCTTACGGTGGTATATGTTCATGAGAGTTCGAGTACTTGACTCATCATATGCACTTGTATTTACAT[G/T]
TAATTGTTTGGGTGAATAGCAAATTTAGTTCCTCAAACTTCACCGAATGATCAATTTGGTCCGCCAGGTTTTATTTTATCCACATAGATCCCCTAAGTAT

Reverse complement sequence

ATACTTAGGGGATCTATGTGGATAAAATAAAACCTGGCGGACCAAATTGATCATTCGGTGAAGTTTGAGGAACTAAATTTGCTATTCACCCAAACAATTA[C/A]
ATGTAAATACAAGTGCATATGATGAGTCAAGTACTCGAACTCTCATGAACATATACCACCGTAAGAAACCTAACATGATGTATTTTCTGATTTTCGATGG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	50.00%	49.90%	0.06%	0.00%	NA
All Indica	2759	48.00%	52.00%	0.07%	0.00%	NA
All Japonica	1512	66.10%	33.80%	0.07%	0.00%	NA
Aus	269	0.40%	99.60%	0.00%	0.00%	NA
Indica I	595	71.90%	27.90%	0.17%	0.00%	NA
Indica II	465	36.30%	63.70%	0.00%	0.00%	NA
Indica III	913	45.20%	54.80%	0.00%	0.00%	NA
Indica Intermediate	786	39.80%	60.10%	0.13%	0.00%	NA
Temperate Japonica	767	70.10%	29.70%	0.13%	0.00%	NA
Tropical Japonica	504	52.60%	47.40%	0.00%	0.00%	NA
Japonica Intermediate	241	81.70%	18.30%	0.00%	0.00%	NA
VI/Aromatic	96	2.10%	97.90%	0.00%	0.00%	NA
Intermediate	90	42.20%	57.80%	0.00%	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
vg0406010273	G -> T	LOC_Os04g11050.1	upstream_gene_variant ; 1227.0bp to feature; MODIFIER	silent_mutation	Average:31.318; most accessible tissue: Callus, score: 63.629	N	N	N	N
vg0406010273	G -> T	LOC_Os04g11060.1	upstream_gene_variant ; 1594.0bp to feature; MODIFIER	silent_mutation	Average:31.318; most accessible tissue: Callus, score: 63.629	N	N	N	N
vg0406010273	G -> T	LOC_Os04g11050-LOC_Os04g11060	intergenic_region ; MODIFIER	silent_mutation	Average:31.318; most accessible tissue: Callus, score: 63.629	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0406010273	6.10E-07	3.77E-16	mr1062	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
vg0406010273	NA	9.36E-08	mr1062	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
vg0406010273	NA	7.87E-06	mr1312	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
vg0406010273	NA	1.91E-09	mr1403	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
vg0406010273	NA	6.46E-06	mr1403	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
vg0406010273	5.89E-07	3.94E-10	mr1525	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
vg0406010273	2.73E-06	2.73E-06	mr1525	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
vg0406010273	NA	5.37E-06	mr1626	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
vg0406010273	NA	8.38E-06	mr1830	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
vg0406010273	NA	4.80E-12	mr1846	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
vg0406010273	NA	6.47E-10	mr1846	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
vg0406010273	9.83E-06	1.08E-07	mr1035_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
vg0406010273	NA	8.48E-07	mr1158_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
vg0406010273	NA	1.72E-09	mr1608_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
vg0406010273	NA	2.06E-07	mr1631_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
vg0406010273	NA	4.68E-06	mr1818_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
vg0406010273	NA	2.83E-07	mr1830_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
vg0406010273	NA	4.87E-15	mr1846_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
vg0406010273	NA	7.70E-14	mr1846_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
vg0406010273	NA	5.92E-06	mr1892_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
vg0406010273	NA	2.24E-06	mr1913_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