Search for Variation information by Variation ID:

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

Detailed information for vg1007055373:

Variant ID: vg1007055373 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 7055373
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, G: 0.00, others allele: 0.00, population size: 191. )

Flanking Sequence (100 bp) in Reference Genome:

CGTTCCAGAACTTCTCATGATTCATATCTTCGGAGTCAACCTCATACAAGTTACCACTTCATGTCATGCGTCAACACTAGCTTGTCATTACTAGGATACC[G/A]
TGTTTGTCATCATAAGAATATCATGCTTGTCATTTACTTCTAACTTGCCACCAACTGCCTCATATTAGCTTTCCTGGTCTCCGGGTGATAGCTACTTCTG

Reverse complement sequence

CAGAAGTAGCTATCACCCGGAGACCAGGAAAGCTAATATGAGGCAGTTGGTGGCAAGTTAGAAGTAAATGACAAGCATGATATTCTTATGATGACAAACA[C/T]
GGTATCCTAGTAATGACAAGCTAGTGTTGACGCATGACATGAAGTGGTAACTTGTATGAGGTTGACTCCGAAGATATGAATCATGAGAAGTTCTGGAACG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	38.10%	6.60%	37.33%	17.96%	NA
All Indica	2759	21.00%	9.20%	43.24%	26.57%	NA
All Japonica	1512	68.10%	1.40%	23.21%	7.28%	NA
Aus	269	24.50%	9.70%	65.80%	0.00%	NA
Indica I	595	6.40%	17.80%	33.78%	42.02%	NA
Indica II	465	14.80%	4.70%	51.83%	28.60%	NA
Indica III	913	36.30%	6.20%	42.94%	14.57%	NA
Indica Intermediate	786	17.90%	8.80%	45.67%	27.61%	NA
Temperate Japonica	767	74.40%	0.70%	16.95%	7.95%	NA
Tropical Japonica	504	58.10%	3.00%	32.54%	6.35%	NA
Japonica Intermediate	241	68.90%	0.40%	23.65%	7.05%	NA
VI/Aromatic	96	74.00%	4.20%	20.83%	1.04%	NA
Intermediate	90	58.90%	10.00%	25.56%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1007055373	G -> A	LOC_Os10g12670.1	upstream_gene_variant ; 4631.0bp to feature; MODIFIER	silent_mutation	Average:8.542; most accessible tissue: Zhenshan97 flower, score: 14.863	N	N	N	N
vg1007055373	G -> A	LOC_Os10g12640.1	downstream_gene_variant ; 2749.0bp to feature; MODIFIER	silent_mutation	Average:8.542; most accessible tissue: Zhenshan97 flower, score: 14.863	N	N	N	N
vg1007055373	G -> A	LOC_Os10g12650.1	downstream_gene_variant ; 1175.0bp to feature; MODIFIER	silent_mutation	Average:8.542; most accessible tissue: Zhenshan97 flower, score: 14.863	N	N	N	N
vg1007055373	G -> A	LOC_Os10g12660.1	intron_variant ; MODIFIER	silent_mutation	Average:8.542; most accessible tissue: Zhenshan97 flower, score: 14.863	N	N	N	N
vg1007055373	G -> DEL	N	N	silent_mutation	Average:8.542; most accessible tissue: Zhenshan97 flower, score: 14.863	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1007055373	3.65E-06	5.22E-10	mr1622	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
vg1007055373	NA	1.21E-06	mr1622	Jap_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