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Detailed information for vg0220738983:

Variant ID: vg0220738983 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 20738983
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 345. )

Flanking Sequence (100 bp) in Reference Genome:

CTTTATAATACAAGCAGGAGGCTTTTGGCTGCACCGCGTGTCTTCATCGATCTCTTTTTCACGCCAATCTTCAGTCAACTTGTCCACAACAACAACAATT[G/A]
TAGACGGAGAGGTAAATTTCTCGGCAATGCAGTTAAAGATGTTACTCAGACTGTCACATTGTGGCTCATATTCAACCCCACCATCAAAAGTGTGTTTGTT

Reverse complement sequence

AACAAACACACTTTTGATGGTGGGGTTGAATATGAGCCACAATGTGACAGTCTGAGTAACATCTTTAACTGCATTGCCGAGAAATTTACCTCTCCGTCTA[C/T]
AATTGTTGTTGTTGTGGACAAGTTGACTGAAGATTGGCGTGAAAAAGAGATCGATGAAGACACGCGGTGCAGCCAAAAGCCTCCTGCTTGTATTATAAAG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	91.30%	8.70%	0.00%	0.00%	NA
All Indica	2759	85.20%	14.80%	0.00%	0.00%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	90.10%	9.90%	0.00%	0.00%	NA
Indica II	465	96.80%	3.20%	0.00%	0.00%	NA
Indica III	913	70.10%	29.90%	0.00%	0.00%	NA
Indica Intermediate	786	92.40%	7.60%	0.00%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	95.60%	4.40%	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
vg0220738983	G -> A	LOC_Os02g34590.1	missense_variant ; p.Thr479Ile; MODERATE	nonsynonymous_codon ; T479I	Average:46.87; most accessible tissue: Callus, score: 82.114	unknown	unknown	TOLERATED	0.18

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0220738983	NA	2.73E-06	mr1875_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
vg0220738983	NA	1.85E-06	mr1908_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