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Detailed information for vg0715293300:

Variant ID: vg0715293300 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 15293300
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, A: 0.04, others allele: 0.00, population size: 55. )

Flanking Sequence (100 bp) in Reference Genome:

CGTTCGCGCGGGACCATGGCGGCGGCGGCGGTGGCGGCAGATCAGAAGGTGGTGACGATGACGAGCCTCCGGGAGGGCTGCGCTTGCGCGGCGCCTCCTG[C/A]
TGCAGCTGCGCCGCCGATGCCGAAGATGGCGGCGGCGCAGAGGGTGGTGGCGGAGCTGAGAGAAGCGTGCGCGACGCCGGCGGCGAGGCTGGCGGAGGTG

Reverse complement sequence

CACCTCCGCCAGCCTCGCCGCCGGCGTCGCGCACGCTTCTCTCAGCTCCGCCACCACCCTCTGCGCCGCCGCCATCTTCGGCATCGGCGGCGCAGCTGCA[G/T]
CAGGAGGCGCCGCGCAAGCGCAGCCCTCCCGGAGGCTCGTCATCGTCACCACCTTCTGATCTGCCGCCACCGCCGCCGCCGCCATGGTCCCGCGCGAACG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	59.50%	40.20%	0.19%	0.06%	NA
All Indica	2759	34.00%	65.70%	0.22%	0.11%	NA
All Japonica	1512	99.20%	0.80%	0.00%	0.00%	NA
Aus	269	87.40%	12.30%	0.37%	0.00%	NA
Indica I	595	35.30%	64.20%	0.34%	0.17%	NA
Indica II	465	15.10%	84.70%	0.22%	0.00%	NA
Indica III	913	32.00%	67.70%	0.22%	0.11%	NA
Indica Intermediate	786	46.60%	53.20%	0.13%	0.13%	NA
Temperate Japonica	767	99.00%	1.00%	0.00%	0.00%	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	87.50%	12.50%	0.00%	0.00%	NA
Intermediate	90	62.20%	35.60%	2.22%	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
vg0715293300	C -> DEL	LOC_Os07g26540.1	N	frameshift_variant	Average:78.974; most accessible tissue: Zhenshan97 young leaf, score: 87.299	N	N	N	N
vg0715293300	C -> A	LOC_Os07g26540.1	missense_variant ; p.Ala29Asp; MODERATE	nonsynonymous_codon ; A29D	Average:78.974; most accessible tissue: Zhenshan97 young leaf, score: 87.299	unknown	unknown	DELETERIOUS	0.04

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0715293300	NA	4.06E-06	mr1058	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
vg0715293300	9.51E-06	1.65E-13	mr1195	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
vg0715293300	NA	3.54E-13	mr1270	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
vg0715293300	NA	2.01E-11	mr1281	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
vg0715293300	NA	1.46E-06	mr1629	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
vg0715293300	NA	3.20E-07	mr1716	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
vg0715293300	NA	2.39E-06	mr1761	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