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Detailed information for vg0523191092:

Variant ID: vg0523191092 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 23191092
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 309. )

Flanking Sequence (100 bp) in Reference Genome:

AGAACGCCAGAAACCCTTTTTAGCAACAAGAAATTGCTGTTTGACAACTACAGTTTCGTAGTGCAGGGACTTGAGAACTGGCCGCATCTTTTTTATCATT[T/G]
CTGTGGTGTCTCTCAACACAAACCATCTGTCAGGTCTCAATATCCTGTCTATTTCAGCTGCTACCTCCATGATGTCACACCTAAAATAAAGATGCAAAGA

Reverse complement sequence

TCTTTGCATCTTTATTTTAGGTGTGACATCATGGAGGTAGCAGCTGAAATAGACAGGATATTGAGACCTGACAGATGGTTTGTGTTGAGAGACACCACAG[A/C]
AATGATAAAAAAGATGCGGCCAGTTCTCAAGTCCCTGCACTACGAAACTGTAGTTGTCAAACAGCAATTTCTTGTTGCTAAAAAGGGTTTCTGGCGTTCT

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	81.40%	17.80%	0.13%	0.61%	NA
All Indica	2759	69.50%	29.30%	0.18%	1.01%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	96.30%	3.70%	0.00%	0.00%	NA
Indica I	595	80.70%	18.20%	0.17%	1.01%	NA
Indica II	465	80.20%	18.70%	0.00%	1.08%	NA
Indica III	913	56.60%	42.30%	0.22%	0.88%	NA
Indica Intermediate	786	69.70%	28.90%	0.25%	1.15%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	73.30%	24.40%	1.11%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0523191092	T -> DEL	LOC_Os05g39520.1	N	frameshift_variant	Average:67.149; most accessible tissue: Zhenshan97 flower, score: 82.948	N	N	N	N
vg0523191092	T -> G	LOC_Os05g39520.1	missense_variant ; p.Glu616Ala; MODERATE	nonsynonymous_codon ; E616A	Average:67.149; most accessible tissue: Zhenshan97 flower, score: 82.948	benign	0.286	TOLERATED	0.10

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0523191092	NA	5.05E-07	mr1336_2	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