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Detailed information for vg0708445190:

Variant ID: vg0708445190 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 8445190
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, others allele: 0.00, population size: 80. )

Flanking Sequence (100 bp) in Reference Genome:

ACACCAAGCGGCCCAGCCAGCGATCTCGCGGCTGGTCGTGGTCCACCGGCTGCCGTCCTCACCTGGGAGGAGCTCCAGGTTGAAATGGGGCGCCTCCTCG[A/T]
GGCTAGTGCTCGCGGCATTGGTCACGAGATTATGGAGGCGAGGTCGGCGGCGGCATCGGCGAACGAGCGCGCCGACCGGCTGGCGCACGACTTGGCGGAG

Reverse complement sequence

CTCCGCCAAGTCGTGCGCCAGCCGGTCGGCGCGCTCGTTCGCCGATGCCGCCGCCGACCTCGCCTCCATAATCTCGTGACCAATGCCGCGAGCACTAGCC[T/A]
CGAGGAGGCGCCCCATTTCAACCTGGAGCTCCTCCCAGGTGAGGACGGCAGCCGGTGGACCACGACCAGCCGCGAGATCGCTGGCTGGGCCGCTTGGTGT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	77.30%	16.20%	5.12%	1.40%	NA
All Indica	2759	62.20%	26.90%	8.55%	2.36%	NA
All Japonica	1512	99.30%	0.50%	0.07%	0.07%	NA
Aus	269	98.50%	1.10%	0.37%	0.00%	NA
Indica I	595	75.80%	4.90%	18.99%	0.34%	NA
Indica II	465	32.70%	58.10%	7.96%	1.29%	NA
Indica III	913	68.60%	29.40%	1.75%	0.33%	NA
Indica Intermediate	786	62.00%	22.30%	8.91%	6.87%	NA
Temperate Japonica	767	99.20%	0.50%	0.13%	0.13%	NA
Tropical Japonica	504	99.60%	0.40%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	81.10%	14.40%	4.44%	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
vg0708445190	A -> DEL	LOC_Os07g14790.1	N	frameshift_variant	Average:61.201; most accessible tissue: Minghui63 young leaf, score: 77.654	N	N	N	N
vg0708445190	A -> T	LOC_Os07g14790.1	missense_variant ; p.Glu292Val; MODERATE	nonsynonymous_codon ; E292V	Average:61.201; most accessible tissue: Minghui63 young leaf, score: 77.654	possibly damaging	1.933	DELETERIOUS	0.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0708445190	NA	7.99E-06	mr1371	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
vg0708445190	4.53E-06	9.65E-08	mr1387	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
vg0708445190	1.92E-06	1.92E-06	mr1387	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
vg0708445190	NA	9.61E-06	mr1432	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
vg0708445190	3.64E-06	NA	mr1516	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
vg0708445190	1.11E-07	1.11E-07	mr1516	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
vg0708445190	NA	4.43E-06	mr1661	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
vg0708445190	NA	1.71E-07	mr1341_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