Search for Variation information by Variation ID:

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

Detailed information for vg1124957503:

Variant ID: vg1124957503 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 24957503
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.94, A: 0.06, others allele: 0.00, population size: 84. )

Flanking Sequence (100 bp) in Reference Genome:

GTACGGTTTCCCGCTCTTGCACTTAAGGACCGTTTCCTTGGAATTTCATCCGAACATAAGACAAGTACGACCACATGGGTGGAATAGGACACCCCTGGCT[A/G]
AGTAACTAGCTTATCAGGGGAGCCTTGATGCCGAGAGACATGTGGATTCGCCGGGGTGGTGTCGGGGAGGACCCCCGGGCTTCCTGGCACAGTATGGTCT

Reverse complement sequence

AGACCATACTGTGCCAGGAAGCCCGGGGGTCCTCCCCGACACCACCCCGGCGAATCCACATGTCTCTCGGCATCAAGGCTCCCCTGATAAGCTAGTTACT[T/C]
AGCCAGGGGTGTCCTATTCCACCCATGTGGTCGTACTTGTCTTATGTTCGGATGAAATTCCAAGGAAACGGTCCTTAAGTGCAAGAGCGGGAAACCGTAC

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	30.00%	0.30%	63.65%	6.07%	NA
All Indica	2759	22.70%	0.20%	76.88%	0.25%	NA
All Japonica	1512	40.40%	0.30%	42.79%	16.47%	NA
Aus	269	28.60%	1.10%	60.59%	9.67%	NA
Indica I	595	18.80%	0.00%	81.01%	0.17%	NA
Indica II	465	45.20%	0.00%	54.84%	0.00%	NA
Indica III	913	12.50%	0.30%	86.86%	0.33%	NA
Indica Intermediate	786	24.00%	0.40%	75.19%	0.38%	NA
Temperate Japonica	767	40.70%	0.30%	49.67%	9.39%	NA
Tropical Japonica	504	38.70%	0.60%	37.50%	23.21%	NA
Japonica Intermediate	241	43.20%	0.00%	31.95%	24.90%	NA
VI/Aromatic	96	63.50%	0.00%	31.25%	5.21%	NA
Intermediate	90	47.80%	0.00%	52.22%	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
vg1124957503	A -> DEL	N	N	silent_mutation	Average:20.569; most accessible tissue: Zhenshan97 root, score: 36.298	N	N	N	N
vg1124957503	A -> G	LOC_Os11g41600.1	upstream_gene_variant ; 4795.0bp to feature; MODIFIER	silent_mutation	Average:20.569; most accessible tissue: Zhenshan97 root, score: 36.298	N	N	N	N
vg1124957503	A -> G	LOC_Os11g41600.2	upstream_gene_variant ; 4795.0bp to feature; MODIFIER	silent_mutation	Average:20.569; most accessible tissue: Zhenshan97 root, score: 36.298	N	N	N	N
vg1124957503	A -> G	LOC_Os11g41600-LOC_Os11g41610	intergenic_region ; MODIFIER	silent_mutation	Average:20.569; most accessible tissue: Zhenshan97 root, score: 36.298	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1124957503	2.73E-06	NA	mr1295_2	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
vg1124957503	5.21E-06	5.21E-06	mr1591_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
vg1124957503	NA	6.22E-06	mr1714_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