Search for Variation information by Variation ID:

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

Detailed information for vg0909772073:

Variant ID: vg0909772073 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 9772073
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCTGAAGCCCAGAATACATGAAGCTCCTATGCTGAGTTTTTATCATCACTATGAATTTCTAAAGATGCCCTGTACACTTGAAAGTTCACTGCTGAATTTT[C/T]
GAGCTTTTACTATTGTTCTAAAATTCTTGAGATGTACTATCAGGAGTTGAAAGTTGAGTGTCTCACTCCATTGCATCTTGTTTTTAAGATACTTAAATAG

Reverse complement sequence

CTATTTAAGTATCTTAAAAACAAGATGCAATGGAGTGAGACACTCAACTTTCAACTCCTGATAGTACATCTCAAGAATTTTAGAACAATAGTAAAAGCTC[G/A]
AAAATTCAGCAGTGAACTTTCAAGTGTACAGGGCATCTTTAGAAATTCATAGTGATGATAAAAACTCAGCATAGGAGCTTCATGTATTCTGGGCTTCAGA

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	82.50%	3.20%	10.26%	4.04%	NA
All Indica	2759	72.20%	5.40%	15.95%	6.42%	NA
All Japonica	1512	97.20%	0.10%	1.85%	0.93%	NA
Aus	269	94.80%	0.00%	5.20%	0.00%	NA
Indica I	595	62.90%	1.30%	26.22%	9.58%	NA
Indica II	465	72.70%	5.60%	15.27%	6.45%	NA
Indica III	913	74.50%	9.30%	10.51%	5.70%	NA
Indica Intermediate	786	76.30%	3.90%	14.89%	4.83%	NA
Temperate Japonica	767	95.40%	0.00%	2.87%	1.69%	NA
Tropical Japonica	504	99.40%	0.00%	0.60%	0.00%	NA
Japonica Intermediate	241	97.90%	0.40%	1.24%	0.41%	NA
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	96.70%	1.10%	2.22%	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
vg0909772073	C -> DEL	N	N	silent_mutation	Average:18.021; most accessible tissue: Zhenshan97 flower, score: 44.193	N	N	N	N
vg0909772073	C -> T	LOC_Os09g15980.1	intron_variant ; MODIFIER	silent_mutation	Average:18.021; most accessible tissue: Zhenshan97 flower, score: 44.193	N	N	N	N
vg0909772073	C -> T	LOC_Os09g15980.2	intron_variant ; MODIFIER	silent_mutation	Average:18.021; most accessible tissue: Zhenshan97 flower, score: 44.193	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0909772073	2.92E-06	5.16E-07	mr1349	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
vg0909772073	1.12E-06	1.12E-06	mr1349	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