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Detailed information for vg0726458639:

Variant ID: vg0726458639 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 26458639
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.70, G: 0.29, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:

AACATCAAAACTGTACAAACCATACAAGAAGAAAAGAGGAAGCATAACAGAGCGAAAGAAAAGACGAAAGAGAGAGAGAAAACAAACAAGAGAGATTACA[T/G]
AAGGTGGAGAGGAGAGGAGAAGGATGCAAGCCAAGACGGAAGAACCGCCTGGTCAGCCAGCTTGAAACGGTTTGCCCAAAGCTTGGCGTCGTTGACGCAG

Reverse complement sequence

CTGCGTCAACGACGCCAAGCTTTGGGCAAACCGTTTCAAGCTGGCTGACCAGGCGGTTCTTCCGTCTTGGCTTGCATCCTTCTCCTCTCCTCTCCACCTT[A/C]
TGTAATCTCTCTTGTTTGTTTTCTCTCTCTCTTTCGTCTTTTCTTTCGCTCTGTTATGCTTCCTCTTTTCTTCTTGTATGGTTTGTACAGTTTTGATGTT

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	58.20%	41.40%	0.13%	0.25%	NA
All Indica	2759	42.80%	56.90%	0.18%	0.14%	NA
All Japonica	1512	98.90%	0.90%	0.00%	0.26%	NA
Aus	269	4.10%	95.90%	0.00%	0.00%	NA
Indica I	595	26.90%	72.60%	0.50%	0.00%	NA
Indica II	465	22.40%	77.60%	0.00%	0.00%	NA
Indica III	913	66.60%	33.20%	0.11%	0.11%	NA
Indica Intermediate	786	39.30%	60.20%	0.13%	0.38%	NA
Temperate Japonica	767	98.80%	1.20%	0.00%	0.00%	NA
Tropical Japonica	504	99.20%	0.40%	0.00%	0.40%	NA
Japonica Intermediate	241	98.30%	0.80%	0.00%	0.83%	NA
VI/Aromatic	96	5.20%	93.80%	1.04%	0.00%	NA
Intermediate	90	64.40%	31.10%	0.00%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0726458639	T -> DEL	N	N	silent_mutation	Average:58.53; most accessible tissue: Minghui63 root, score: 79.298	N	N	N	N
vg0726458639	T -> G	LOC_Os07g44280.1	upstream_gene_variant ; 1018.0bp to feature; MODIFIER	silent_mutation	Average:58.53; most accessible tissue: Minghui63 root, score: 79.298	N	N	N	N
vg0726458639	T -> G	LOC_Os07g44280-LOC_Os07g44290	intergenic_region ; MODIFIER	silent_mutation	Average:58.53; most accessible tissue: Minghui63 root, score: 79.298	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0726458639	NA	5.54E-06	mr1086	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
vg0726458639	NA	8.51E-06	mr1104	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
vg0726458639	NA	3.88E-09	mr1213	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
vg0726458639	NA	1.00E-06	mr1246	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
vg0726458639	NA	1.62E-07	mr1354	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
vg0726458639	NA	1.24E-12	mr1806	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
vg0726458639	NA	7.09E-06	mr1246_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
vg0726458639	NA	8.93E-11	mr1806_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