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Detailed information for vg0818511687:

Variant ID: vg0818511687 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 18511687
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.66, A: 0.34, others allele: 0.00, population size: 92. )

Flanking Sequence (100 bp) in Reference Genome:


TTAGCATAATTATTTTAATGTGACATATTATTAAAACTATTTAAACTAATTGTTAGTTTTTTTCTCAATGCATAGACGATGGCAGATAGATCATGGATGC[A/G]
TAGAGAGAGATATCATGCGTCATATATTGAAGGAGTCGACATATTTATGAAAGCTGCGAGGAAAAATGCTGTAGCTAAGAAGACAAATGAAATTAGATGT

Reverse complement sequence

ACATCTAATTTCATTTGTCTTCTTAGCTACAGCATTTTTCCTCGCAGCTTTCATAAATATGTCGACTCCTTCAATATATGACGCATGATATCTCTCTCTA[T/C]
GCATCCATGATCTATCTGCCATCGTCTATGCATTGAGAAAAAAACTAACAATTAGTTTAAATAGTTTTAATAATATGTCACATTAAAATAATTATGCTAA

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 53.60% 3.00% 23.09% 20.27% NA
All Indica  2759 31.90% 5.00% 28.67% 34.40% NA
All Japonica  1512 88.40% 0.10% 11.51% 0.07% NA
Aus  269 61.70% 0.40% 37.55% 0.37% NA
Indica I  595 32.60% 6.90% 24.71% 35.80% NA
Indica II  465 79.60% 0.60% 12.90% 6.88% NA
Indica III  913 5.00% 8.20% 35.27% 51.48% NA
Indica Intermediate  786 34.40% 2.50% 33.33% 29.77% NA
Temperate Japonica  767 99.20% 0.00% 0.78% 0.00% NA
Tropical Japonica  504 70.60% 0.20% 28.97% 0.20% NA
Japonica Intermediate  241 90.90% 0.00% 9.13% 0.00% NA
VI/Aromatic  96 91.70% 0.00% 8.33% 0.00% NA
Intermediate  90 72.20% 1.10% 18.89% 7.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0818511687 A -> G LOC_Os08g30110.1 missense_variant ; p.His8Arg; MODERATE nonsynonymous_codon ; H8R Average:25.906; most accessible tissue: Callus, score: 34.806 unknown unknown DELETERIOUS 0.05
vg0818511687 A -> DEL LOC_Os08g30110.1 N frameshift_variant Average:25.906; most accessible tissue: Callus, score: 34.806 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0818511687 NA 7.59E-06 mr1042 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
vg0818511687 NA 6.81E-06 mr1043 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
vg0818511687 3.01E-09 3.01E-09 mr1266 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
vg0818511687 NA 6.15E-07 mr1345 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
vg0818511687 NA 9.24E-09 mr1399 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
vg0818511687 NA 3.27E-07 mr1845 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
vg0818511687 3.23E-06 3.23E-06 mr1873 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
vg0818511687 NA 9.44E-07 mr1045_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
vg0818511687 NA 4.39E-07 mr1047_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
vg0818511687 NA 3.35E-06 mr1060_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
vg0818511687 NA 1.90E-08 mr1063_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
vg0818511687 NA 1.96E-09 mr1221_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
vg0818511687 NA 2.30E-06 mr1268_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
vg0818511687 NA 4.08E-06 mr1296_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
vg0818511687 NA 6.33E-06 mr1296_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
vg0818511687 6.63E-07 NA mr1301_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
vg0818511687 NA 1.90E-09 mr1327_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
vg0818511687 NA 7.45E-11 mr1327_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
vg0818511687 NA 2.07E-08 mr1378_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
vg0818511687 1.08E-06 NA mr1410_2 Jap_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
vg0818511687 NA 1.08E-08 mr1446_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
vg0818511687 NA 3.61E-10 mr1546_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
vg0818511687 NA 7.35E-10 mr1627_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
vg0818511687 NA 2.93E-12 mr1739_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
vg0818511687 NA 4.58E-06 mr1825_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