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Detailed information for vg0432965430:

Variant ID: vg0432965430 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 32965430
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

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

Flanking Sequence (100 bp) in Reference Genome:

TTGTCCACTCTGGATTTGTCAGACAATAACTTTCATGGAGAAATTCCGATGTCACTGTGCAGCATCAAACACATGAAGGACTTGAGCTTATCAAACAATA[A/T]
TTTTTCTGGTAAAATGCCGACTTGTGTGTTCACTGATTTTCTTGAGCTGTGGACCTTGAGTGCCTCAAACAACCAGCTTGGAGGTCTGGTGTTTGGTGGG

Reverse complement sequence

CCCACCAAACACCAGACCTCCAAGCTGGTTGTTTGAGGCACTCAAGGTCCACAGCTCAAGAAAATCAGTGAACACACAAGTCGGCATTTTACCAGAAAAA[T/A]
TATTGTTTGATAAGCTCAAGTCCTTCATGTGTTTGATGCTGCACAGTGACATCGGAATTTCTCCATGAAAGTTATTGTCTGACAAATCCAGAGTGGACAA

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	97.50%	2.50%	0.00%	0.00%	NA
All Indica	2759	99.90%	0.10%	0.00%	0.00%	NA
All Japonica	1512	92.70%	7.30%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.50%	0.50%	0.00%	0.00%	NA
Temperate Japonica	767	89.60%	10.40%	0.00%	0.00%	NA
Tropical Japonica	504	99.00%	1.00%	0.00%	0.00%	NA
Japonica Intermediate	241	89.20%	10.80%	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
vg0432965430	A -> T	LOC_Os04g55420.1	missense_variant ; p.Asn504Ile; MODERATE	nonsynonymous_codon	Average:61.667; most accessible tissue: Callus, score: 83.491	unknown	unknown	DELETERIOUS	0.05

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0432965430	3.94E-09	3.06E-06	mr1101	Jap_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