Search for Variation information by Variation ID:

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

Detailed information for vg0709146977:

Variant ID: vg0709146977 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 9146977
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.97, A: 0.02, others allele: 0.00, population size: 119. )

Flanking Sequence (100 bp) in Reference Genome:

TAGGTGGCGGCGGCCATCAGAGGTTCATCCTTAGCAGAATTGGCTATGGTGAGAGCAAACGCTTGGCCGATCCCAATCTCATCCCAGTGGACTTTCTTAC[T/A]
AGCCGATATGCGTTGGTACCAGGTGGTCCAACTCTTATCAGGGGTAGGCTTTTCGAGAGATGGCCAAGACTTGAAGGTATTCTTCCAGTGACCCAGGTTA

Reverse complement sequence

TAACCTGGGTCACTGGAAGAATACCTTCAAGTCTTGGCCATCTCTCGAAAAGCCTACCCCTGATAAGAGTTGGACCACCTGGTACCAACGCATATCGGCT[A/T]
GTAAGAAAGTCCACTGGGATGAGATTGGGATCGGCCAAGCGTTTGCTCTCACCATAGCCAATTCTGCTAAGGATGAACCTCTGATGGCCGCCGCCACCTA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	56.20%	39.20%	2.24%	2.31%	NA
All Indica	2759	30.80%	64.70%	3.08%	1.38%	NA
All Japonica	1512	93.70%	1.20%	0.66%	4.50%	NA
Aus	269	90.30%	6.70%	2.97%	0.00%	NA
Indica I	595	67.70%	25.90%	3.03%	3.36%	NA
Indica II	465	16.10%	77.80%	5.16%	0.86%	NA
Indica III	913	9.60%	88.50%	1.64%	0.22%	NA
Indica Intermediate	786	36.30%	58.70%	3.56%	1.53%	NA
Temperate Japonica	767	96.60%	1.40%	1.04%	0.91%	NA
Tropical Japonica	504	88.50%	0.80%	0.00%	10.71%	NA
Japonica Intermediate	241	95.00%	1.20%	0.83%	2.90%	NA
VI/Aromatic	96	96.90%	1.00%	0.00%	2.08%	NA
Intermediate	90	60.00%	35.60%	3.33%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0709146977	T -> DEL	LOC_Os07g15760.1	N	frameshift_variant	Average:20.985; most accessible tissue: Minghui63 flower, score: 40.98	N	N	N	N
vg0709146977	T -> A	LOC_Os07g15760.1	missense_variant&splice_region_variant ; p.Asn96Tyr; MODERATE	nonsynonymous_codon	Average:20.985; most accessible tissue: Minghui63 flower, score: 40.98	unknown	unknown	DELETERIOUS	0.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0709146977	NA	7.49E-15	mr1170	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
vg0709146977	NA	7.74E-07	mr1170	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
vg0709146977	NA	1.66E-14	mr1316	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
vg0709146977	NA	4.69E-06	mr1316	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
vg0709146977	NA	2.49E-07	mr1716	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