Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0403322252:

Variant ID: vg0403322252 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 3322252
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, T: 0.04, others allele: 0.00, population size: 66. )

Flanking Sequence (100 bp) in Reference Genome:

CTCCACGCCCTGTTGCATCTCCAACACAGCAACAGCCTGCCAAGAGGGAGCAAGGCAGTAAGCCCGGGGTGTGCTTCAACTGTGGAGACCCAGGACATTA[C/T]
GCTGACAAGTGTCCGAAGCCCCGCCGCGTGAAGGTCGTCCCTGCCCAGAACAACCCCTCCGCACCCGCAGCCAAGGCTCGTGTCAACCATGTTGCTGCTG

Reverse complement sequence

CAGCAGCAACATGGTTGACACGAGCCTTGGCTGCGGGTGCGGAGGGGTTGTTCTGGGCAGGGACGACCTTCACGCGGCGGGGCTTCGGACACTTGTCAGC[G/A]
TAATGTCCTGGGTCTCCACAGTTGAAGCACACCCCGGGCTTACTGCCTTGCTCCCTCTTGGCAGGCTGTTGCTGTGTTGGAGATGCAACAGGGCGTGGAG

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	39.30%	4.60%	14.56%	41.49%	NA
All Indica	2759	29.80%	2.60%	19.79%	47.88%	NA
All Japonica	1512	62.40%	0.10%	1.79%	35.71%	NA
Aus	269	15.20%	51.30%	23.05%	10.41%	NA
Indica I	595	18.50%	0.80%	17.65%	63.03%	NA
Indica II	465	40.60%	0.20%	11.18%	47.96%	NA
Indica III	913	28.00%	3.50%	25.08%	43.37%	NA
Indica Intermediate	786	33.80%	4.20%	20.36%	41.60%	NA
Temperate Japonica	767	90.00%	0.00%	0.39%	9.65%	NA
Tropical Japonica	504	24.40%	0.40%	2.78%	72.42%	NA
Japonica Intermediate	241	53.90%	0.00%	4.15%	41.91%	NA
VI/Aromatic	96	19.80%	4.20%	39.58%	36.46%	NA
Intermediate	90	37.80%	4.40%	16.67%	41.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0403322252	C -> DEL	LOC_Os04g06360.1	N	frameshift_variant	Average:35.975; most accessible tissue: Minghui63 young leaf, score: 72.408	N	N	N	N
vg0403322252	C -> T	LOC_Os04g06360.1	synonymous_variant ; p.Tyr818Tyr; LOW	synonymous_codon	Average:35.975; most accessible tissue: Minghui63 young leaf, score: 72.408	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0403322252	NA	1.61E-06	mr1008	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
vg0403322252	NA	2.69E-06	mr1009	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
vg0403322252	2.47E-06	8.70E-07	mr1946	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
vg0403322252	NA	7.60E-07	mr1008_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