Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923).

Detailed information for vg0430121316:

Variant ID: vg0430121316 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 30121316
Reference Allele: T	Alternative Allele: A
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: 286. )

Flanking Sequence (100 bp) in Reference Genome:

CTACCCTGATTCCTTGTCGCTCCACCTTTGTGGTACTTCGGTATCTATGCTCTCTGAGCGCGTATAAGAACTATTCCACATACACCGTTGTTTGTCGAAA[T/A]
TTTGGGAAATGGGTTTGAGAAGCCTTGAAAACCCAACATGTGGTGTCGGTGTGTTTGAAAATAAAATGAATTGTGAAAACTCGCGATGCGGGTGTTGTGC

Reverse complement sequence

GCACAACACCCGCATCGCGAGTTTTCACAATTCATTTTATTTTCAAACACACCGACACCACATGTTGGGTTTTCAAGGCTTCTCAAACCCATTTCCCAAA[A/T]
TTTCGACAAACAACGGTGTATGTGGAATAGTTCTTATACGCGCTCAGAGAGCATAGATACCGAAGTACCACAAAGGTGGAGCGACAAGGAATCAGGGTAG

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	68.60%	31.40%	0.00%	0.00%	NA
All Indica	2759	95.10%	4.90%	0.00%	0.00%	NA
All Japonica	1512	20.80%	79.20%	0.00%	0.00%	NA
Aus	269	94.40%	5.60%	0.00%	0.00%	NA
Indica I	595	98.80%	1.20%	0.00%	0.00%	NA
Indica II	465	92.70%	7.30%	0.00%	0.00%	NA
Indica III	913	95.70%	4.30%	0.00%	0.00%	NA
Indica Intermediate	786	93.00%	7.00%	0.00%	0.00%	NA
Temperate Japonica	767	5.10%	94.90%	0.00%	0.00%	NA
Tropical Japonica	504	29.20%	70.80%	0.00%	0.00%	NA
Japonica Intermediate	241	53.10%	46.90%	0.00%	0.00%	NA
VI/Aromatic	96	1.00%	99.00%	0.00%	0.00%	NA
Intermediate	90	55.60%	44.40%	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
vg0430121316	T -> A	LOC_Os04g50910.1	upstream_gene_variant ; 1579.0bp to feature; MODIFIER	silent_mutation	Average:33.467; most accessible tissue: Minghui63 panicle, score: 46.754	N	N	N	N
vg0430121316	T -> A	LOC_Os04g50910-LOC_Os04g50920	intergenic_region ; MODIFIER	silent_mutation	Average:33.467; most accessible tissue: Minghui63 panicle, score: 46.754	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0430121316	7.22E-07	7.22E-07	mr1877_2	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