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

Detailed information for vg0434551164:

Variant ID: vg0434551164 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 34551164
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.79, T: 0.21, others allele: 0.00, population size: 101. )

Flanking Sequence (100 bp) in Reference Genome:


TCTCGTTTCTCCCCCAGCTTCCTTTTCCCAACAAGCCAAAACACCAAGCCACCGTACAAATGAGAGAGGAGGCCGCGGGCGGATCTGGCAGCGGTGATGG[T/C]
GGCCCTCGCGAACGCACACGGATCTGATGGTGGAGGTGCTCGCGGAAGAAGGCCACAGCAGCGGTAGATTTGGCGACGGCGGCATCTCGCATGGATCTGT

Reverse complement sequence

ACAGATCCATGCGAGATGCCGCCGTCGCCAAATCTACCGCTGCTGTGGCCTTCTTCCGCGAGCACCTCCACCATCAGATCCGTGTGCGTTCGCGAGGGCC[A/G]
CCATCACCGCTGCCAGATCCGCCCGCGGCCTCCTCTCTCATTTGTACGGTGGCTTGGTGTTTTGGCTTGTTGGGAAAAGGAAGCTGGGGGAGAAACGAGA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 61.00% 38.30% 0.00% 0.68% NA
All Indica  2759 96.30% 2.80% 0.00% 0.91% NA
All Japonica  1512 11.60% 88.10% 0.00% 0.33% NA
Aus  269 1.10% 98.90% 0.00% 0.00% NA
Indica I  595 97.80% 1.00% 0.00% 1.18% NA
Indica II  465 97.40% 1.10% 0.00% 1.51% NA
Indica III  913 98.60% 1.30% 0.00% 0.11% NA
Indica Intermediate  786 92.00% 6.70% 0.00% 1.27% NA
Temperate Japonica  767 4.40% 95.30% 0.00% 0.26% NA
Tropical Japonica  504 6.90% 92.70% 0.00% 0.40% NA
Japonica Intermediate  241 44.00% 55.60% 0.00% 0.41% NA
VI/Aromatic  96 5.20% 94.80% 0.00% 0.00% NA
Intermediate  90 46.70% 51.10% 0.00% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0434551164 T -> C LOC_Os04g58010.1 missense_variant ; p.Thr275Ala; MODERATE nonsynonymous_codon ; T275A Average:56.144; most accessible tissue: Zhenshan97 young leaf, score: 81.6 unknown unknown TOLERATED 0.73
vg0434551164 T -> DEL LOC_Os04g58010.1 N frameshift_variant Average:56.144; most accessible tissue: Zhenshan97 young leaf, score: 81.6 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0434551164 NA 2.26E-14 mr1013 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
vg0434551164 NA 9.05E-13 mr1031 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
vg0434551164 NA 3.01E-27 mr1037 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
vg0434551164 NA 2.70E-13 mr1056 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
vg0434551164 NA 6.03E-41 mr1458 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
vg0434551164 NA 3.92E-23 mr1571 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
vg0434551164 NA 5.83E-06 mr1691 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
vg0434551164 2.31E-06 NA mr1693 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
vg0434551164 NA 9.26E-10 mr1693 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
vg0434551164 NA 1.40E-31 mr1037_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
vg0434551164 NA 1.48E-21 mr1164_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
vg0434551164 NA 1.77E-06 mr1496_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
vg0434551164 NA 1.65E-43 mr1509_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
vg0434551164 NA 5.67E-35 mr1571_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
vg0434551164 NA 1.47E-30 mr1580_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
vg0434551164 NA 2.27E-30 mr1825_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
vg0434551164 NA 2.54E-27 mr1943_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