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Detailed information for vg0800344884:

Variant ID: vg0800344884 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 344884
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.90, G: 0.11, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:


TGTGCCTTTCCAAACAATGGCAAAGGTAGCAGAGTGATAGTAACCACACGAGTGAAAGATGTGGCCAGGTTGGCATGTGGCAAGGATGGACAAATTTACA[A/G]
AATACAGCCTCTGAACAATAAGGACTCAAGAAAGTTATTCTTCGATAGAGTATTTAGGCCTGAAGATAGTTGTGTCCTGCAGTATGAAGAAATTTCAACT

Reverse complement sequence

AGTTGAAATTTCTTCATACTGCAGGACACAACTATCTTCAGGCCTAAATACTCTATCGAAGAATAACTTTCTTGAGTCCTTATTGTTCAGAGGCTGTATT[T/C]
TGTAAATTTGTCCATCCTTGCCACATGCCAACCTGGCCACATCTTTCACTCGTGTGGTTACTATCACTCTGCTACCTTTGCCATTGTTTGGAAAGGCACA

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 55.90% 43.90% 0.11% 0.11% NA
All Indica  2759 38.90% 60.70% 0.18% 0.18% NA
All Japonica  1512 87.20% 12.80% 0.00% 0.00% NA
Aus  269 65.10% 34.90% 0.00% 0.00% NA
Indica I  595 59.00% 40.50% 0.00% 0.50% NA
Indica II  465 23.40% 76.30% 0.22% 0.00% NA
Indica III  913 33.50% 66.30% 0.11% 0.11% NA
Indica Intermediate  786 39.10% 60.40% 0.38% 0.13% NA
Temperate Japonica  767 97.10% 2.90% 0.00% 0.00% NA
Tropical Japonica  504 71.40% 28.60% 0.00% 0.00% NA
Japonica Intermediate  241 88.80% 11.20% 0.00% 0.00% NA
VI/Aromatic  96 18.80% 81.20% 0.00% 0.00% NA
Intermediate  90 61.10% 38.90% 0.00% 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
vg0800344884 A -> G LOC_Os08g01580.1 missense_variant ; p.Lys324Arg; MODERATE nonsynonymous_codon ; K324R Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 benign 0.455 TOLERATED 0.89
vg0800344884 A -> DEL LOC_Os08g01580.1 N frameshift_variant Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0800344884 1.34E-06 8.47E-11 mr1277 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
vg0800344884 3.32E-07 4.60E-06 mr1277 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
vg0800344884 1.99E-22 4.37E-45 mr1746 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
vg0800344884 6.09E-20 4.49E-25 mr1746 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
vg0800344884 NA 1.16E-13 mr1746 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
vg0800344884 NA 7.62E-13 mr1769 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
vg0800344884 NA 3.59E-12 mr1055_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
vg0800344884 7.12E-12 1.74E-14 mr1277_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
vg0800344884 4.25E-10 4.84E-07 mr1277_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
vg0800344884 8.15E-08 NA mr1298_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
vg0800344884 NA 1.94E-07 mr1676_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
vg0800344884 NA 6.53E-06 mr1702_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
vg0800344884 9.01E-07 NA mr1731_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
vg0800344884 2.65E-26 7.88E-57 mr1746_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
vg0800344884 5.69E-25 2.33E-33 mr1746_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
vg0800344884 3.20E-06 1.25E-11 mr1746_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
vg0800344884 NA 2.96E-13 mr1769_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