Search for Variation information by Variation ID:

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

Detailed information for vg0403780245:

Variant ID: vg0403780245 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 3780245
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.67, C: 0.33, others allele: 0.00, population size: 61. )

Flanking Sequence (100 bp) in Reference Genome:

AATAAAAGCATCCACAACCAACCTTCTAAACATGTTAGAGTTAAGGCCCGAAAGGCGGTTGTGGTCCTCGCACGAGGGGTCAATACTAATCGAACATGAT[T/C]
CTGGGGATTCCTTATGTGAGCATGAATCCTGGGGGATTTTGAAAAAGAATATTTCATGCTCATTTGTGGAGTTCTCATCTTCTAGGGTTGATGTCTCAAG

Reverse complement sequence

CTTGAGACATCAACCCTAGAAGATGAGAACTCCACAAATGAGCATGAAATATTCTTTTTCAAAATCCCCCAGGATTCATGCTCACATAAGGAATCCCCAG[A/G]
ATCATGTTCGATTAGTATTGACCCCTCGTGCGAGGACCACAACCGCCTTTCGGGCCTTAACTCTAACATGTTTAGAAGGTTGGTTGTGGATGCTTTTATT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	59.00%	20.90%	0.68%	19.47%	NA
All Indica	2759	87.60%	5.70%	0.36%	6.34%	NA
All Japonica	1512	6.00%	45.80%	0.99%	47.22%	NA
Aus	269	50.20%	43.90%	2.23%	3.72%	NA
Indica I	595	98.00%	0.80%	0.00%	1.18%	NA
Indica II	465	80.90%	5.80%	0.43%	12.90%	NA
Indica III	913	87.40%	6.80%	0.66%	5.15%	NA
Indica Intermediate	786	84.10%	7.90%	0.25%	7.76%	NA
Temperate Japonica	767	2.90%	65.70%	0.91%	30.51%	NA
Tropical Japonica	504	9.90%	15.10%	0.79%	74.21%	NA
Japonica Intermediate	241	7.90%	46.50%	1.66%	43.98%	NA
VI/Aromatic	96	88.50%	2.10%	0.00%	9.38%	NA
Intermediate	90	65.60%	20.00%	1.11%	13.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0403780245	T -> C	LOC_Os04g07130.1	upstream_gene_variant ; 3036.0bp to feature; MODIFIER	silent_mutation	Average:17.087; most accessible tissue: Zhenshan97 root, score: 49.075	N	N	N	N
vg0403780245	T -> C	LOC_Os04g07120.1	downstream_gene_variant ; 129.0bp to feature; MODIFIER	silent_mutation	Average:17.087; most accessible tissue: Zhenshan97 root, score: 49.075	N	N	N	N
vg0403780245	T -> C	LOC_Os04g07110-LOC_Os04g07120	intergenic_region ; MODIFIER	silent_mutation	Average:17.087; most accessible tissue: Zhenshan97 root, score: 49.075	N	N	N	N
vg0403780245	T -> DEL	N	N	silent_mutation	Average:17.087; most accessible tissue: Zhenshan97 root, score: 49.075	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0403780245	2.53E-06	NA	mr1611	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
vg0403780245	NA	7.58E-09	mr1763	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
vg0403780245	NA	9.35E-06	mr1837	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