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Detailed information for vg0710418364:

Variant ID: vg0710418364 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 10418364
Reference Allele: GAlternative Allele: A,T
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.71, G: 0.28, others allele: 0.00, population size: 80. )

Flanking Sequence (100 bp) in Reference Genome:


TCGGCCCGTTTAAAAGGGCAGTCGGCGGTTACACGCATCTCTTTGTGGCTATCGACAAATTCTCCAAGTGGATTGAGGCTAAACCGGTCATCACGATCAC[G/A,T]
GCAAATAAAGCTAGAGATTTTTTCATCAACATTGTGCATCGGTTTGGGGAACCTAATCGGATCATCACTGATAATGGCACTCAATTCACTGGCGGAGCAT

Reverse complement sequence

ATGCTCCGCCAGTGAATTGAGTGCCATTATCAGTGATGATCCGATTAGGTTCCCCAAACCGATGCACAATGTTGATGAAAAAATCTCTAGCTTTATTTGC[C/T,A]
GTGATCGTGATGACCGGTTTAGCCTCAATCCACTTGGAGAATTTGTCGATAGCCACAAAGAGATGCGTGTAACCGCCGACTGCCCTTTTAAACGGGCCGA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 39.50% 2.80% 21.77% 35.89% T: 0.04%
All Indica  2759 7.80% 4.60% 29.10% 58.43% T: 0.07%
All Japonica  1512 95.40% 0.00% 3.51% 1.06% NA
Aus  269 54.60% 2.20% 31.23% 11.90% NA
Indica I  595 11.30% 3.90% 29.75% 55.13% NA
Indica II  465 6.70% 2.80% 23.01% 67.53% NA
Indica III  913 1.50% 7.60% 29.35% 61.34% T: 0.22%
Indica Intermediate  786 13.20% 2.70% 31.93% 52.16% NA
Temperate Japonica  767 98.20% 0.00% 1.17% 0.65% NA
Tropical Japonica  504 90.70% 0.00% 7.54% 1.79% NA
Japonica Intermediate  241 96.70% 0.00% 2.49% 0.83% NA
VI/Aromatic  96 18.80% 1.00% 75.00% 5.21% NA
Intermediate  90 45.60% 1.10% 18.89% 34.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0710418364 G -> DEL LOC_Os07g17630.1 N frameshift_variant Average:19.443; most accessible tissue: Zhenshan97 root, score: 32.766 N N N N
vg0710418364 G -> A LOC_Os07g17630.1 synonymous_variant ; p.Thr1058Thr; LOW synonymous_codon Average:19.443; most accessible tissue: Zhenshan97 root, score: 32.766 N N N N
vg0710418364 G -> T LOC_Os07g17630.1 synonymous_variant ; p.Thr1058Thr; LOW synonymous_codon Average:19.443; most accessible tissue: Zhenshan97 root, score: 32.766 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0710418364 NA 5.88E-08 mr1249 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
vg0710418364 NA 2.50E-07 mr1559 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
vg0710418364 NA 1.12E-08 mr1074_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
vg0710418364 NA 2.79E-32 mr1081_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
vg0710418364 NA 6.51E-09 mr1084_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
vg0710418364 NA 1.98E-06 mr1146_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
vg0710418364 NA 1.10E-18 mr1148_2 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
vg0710418364 NA 9.62E-07 mr1148_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
vg0710418364 NA 7.45E-13 mr1151_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
vg0710418364 NA 1.71E-11 mr1198_2 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
vg0710418364 NA 2.47E-07 mr1205_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
vg0710418364 NA 2.85E-13 mr1217_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
vg0710418364 NA 4.95E-09 mr1222_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
vg0710418364 NA 9.36E-07 mr1222_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
vg0710418364 NA 3.75E-18 mr1239_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
vg0710418364 NA 4.14E-33 mr1256_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
vg0710418364 NA 1.59E-06 mr1256_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
vg0710418364 NA 1.26E-08 mr1275_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
vg0710418364 NA 3.50E-21 mr1298_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
vg0710418364 NA 1.11E-07 mr1376_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
vg0710418364 NA 2.17E-06 mr1405_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
vg0710418364 NA 3.26E-08 mr1431_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
vg0710418364 NA 4.64E-06 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
vg0710418364 NA 5.61E-07 mr1548_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
vg0710418364 NA 4.90E-06 mr1551_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
vg0710418364 NA 1.28E-15 mr1575_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
vg0710418364 NA 3.15E-09 mr1660_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
vg0710418364 NA 3.98E-07 mr1668_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
vg0710418364 NA 6.83E-06 mr1696_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
vg0710418364 NA 1.06E-21 mr1698_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
vg0710418364 NA 3.82E-20 mr1731_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
vg0710418364 NA 4.54E-10 mr1835_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
vg0710418364 NA 3.87E-06 mr1869_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
vg0710418364 NA 6.17E-21 mr1922_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
vg0710418364 NA 1.50E-21 mr1924_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
vg0710418364 NA 1.04E-09 mr1940_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
vg0710418364 NA 5.61E-16 mr1950_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