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Detailed information for vg0723562063:

Variant ID: vg0723562063 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 23562063
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:


TGCACTTCATTTTGATGGTTTAATTAATAAAATATTTATAGTTTCTAGTAAATAAATATAATTAATATGGGAAGAGGTTGTCTTTTAGCAGTGCACAACA[G/A]
AGAAGTTAGGGTTTTAAGCAAATTGATGTAGATTGTGATGAGTGGACTGTAGGGAAGTGATAGTAGTCAACGGTGGAACCACCTCCCGAGCTTTTGGGAA

Reverse complement sequence

TTCCCAAAAGCTCGGGAGGTGGTTCCACCGTTGACTACTATCACTTCCCTACAGTCCACTCATCACAATCTACATCAATTTGCTTAAAACCCTAACTTCT[C/T]
TGTTGTGCACTGCTAAAAGACAACCTCTTCCCATATTAATTATATTTATTTACTAGAAACTATAAATATTTTATTAATTAAACCATCAAAATGAAGTGCA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 70.00% 29.80% 0.21% 0.00% NA
All Indica  2759 94.70% 5.10% 0.18% 0.00% NA
All Japonica  1512 20.40% 79.50% 0.07% 0.00% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 96.00% 3.70% 0.34% 0.00% NA
Indica II  465 92.00% 8.00% 0.00% 0.00% NA
Indica III  913 98.50% 1.20% 0.33% 0.00% NA
Indica Intermediate  786 90.80% 9.20% 0.00% 0.00% NA
Temperate Japonica  767 9.80% 90.10% 0.13% 0.00% NA
Tropical Japonica  504 28.40% 71.60% 0.00% 0.00% NA
Japonica Intermediate  241 37.80% 62.20% 0.00% 0.00% NA
VI/Aromatic  96 71.90% 28.10% 0.00% 0.00% NA
Intermediate  90 56.70% 38.90% 4.44% 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
vg0723562063 G -> A LOC_Os07g39330.1 upstream_gene_variant ; 108.0bp to feature; MODIFIER silent_mutation Average:52.416; most accessible tissue: Callus, score: 87.893 N N N N
vg0723562063 G -> A LOC_Os07g39340.1 upstream_gene_variant ; 4072.0bp to feature; MODIFIER silent_mutation Average:52.416; most accessible tissue: Callus, score: 87.893 N N N N
vg0723562063 G -> A LOC_Os07g39320.1 downstream_gene_variant ; 1195.0bp to feature; MODIFIER silent_mutation Average:52.416; most accessible tissue: Callus, score: 87.893 N N N N
vg0723562063 G -> A LOC_Os07g39320-LOC_Os07g39330 intergenic_region ; MODIFIER silent_mutation Average:52.416; most accessible tissue: Callus, score: 87.893 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0723562063 NA 4.76E-21 mr1163 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
vg0723562063 1.22E-06 2.00E-48 mr1563 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
vg0723562063 8.10E-06 8.05E-07 mr1563 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
vg0723562063 NA 4.49E-06 mr1980 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
vg0723562063 1.84E-07 1.84E-07 mr1261_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
vg0723562063 NA 8.24E-06 mr1519_2 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
vg0723562063 NA 1.26E-11 mr1533_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
vg0723562063 2.22E-09 6.94E-80 mr1563_2 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
vg0723562063 9.86E-09 5.21E-10 mr1563_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
vg0723562063 NA 5.23E-08 mr1607_2 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
vg0723562063 NA 2.75E-08 mr1865_2 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
vg0723562063 NA 2.26E-08 mr1980_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