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Detailed information for vg0724427664:

Variant ID: vg0724427664 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 24427664
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.70, T: 0.31, others allele: 0.00, population size: 186. )

Flanking Sequence (100 bp) in Reference Genome:


AATTCAAAGATACTGGGAGCTAGAGATGAACCCATAATTACCATGGTTGAGCACATAAGGACAAAAATGATGGGTGATTTCAATAATAAGAGGGAAGGTG[T/C]
AGAAAGGGACAATTGGCAAATCCCACCAAATATATTAAAGAAGCTTGAGGCAGAGAAGAGAGAGGCAAGATATTGCAAATCTGTGTGTGCTGGTAGGGGC

Reverse complement sequence

GCCCCTACCAGCACACACAGATTTGCAATATCTTGCCTCTCTCTTCTCTGCCTCAAGCTTCTTTAATATATTTGGTGGGATTTGCCAATTGTCCCTTTCT[A/G]
CACCTTCCCTCTTATTATTGAAATCACCCATCATTTTTGTCCTTATGTGCTCAACCATGGTAATTATGGGTTCATCTCTAGCTCCCAGTATCTTTGAATT

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 83.00% 14.90% 2.05% 0.00% NA
All Indica  2759 97.40% 1.90% 0.72% 0.00% NA
All Japonica  1512 55.40% 40.20% 4.43% 0.00% NA
Aus  269 92.90% 7.10% 0.00% 0.00% NA
Indica I  595 98.30% 1.70% 0.00% 0.00% NA
Indica II  465 96.60% 1.90% 1.51% 0.00% NA
Indica III  913 99.30% 0.30% 0.33% 0.00% NA
Indica Intermediate  786 94.80% 3.90% 1.27% 0.00% NA
Temperate Japonica  767 37.90% 61.10% 0.91% 0.00% NA
Tropical Japonica  504 83.50% 7.50% 8.93% 0.00% NA
Japonica Intermediate  241 51.90% 41.90% 6.22% 0.00% NA
VI/Aromatic  96 88.50% 10.40% 1.04% 0.00% NA
Intermediate  90 72.20% 17.80% 10.00% 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
vg0724427664 T -> C LOC_Os07g40760.1 missense_variant ; p.Val925Ala; MODERATE nonsynonymous_codon ; V925A Average:9.595; most accessible tissue: Minghui63 root, score: 13.235 unknown unknown TOLERATED 1.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0724427664 1.29E-07 NA mr1138 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
vg0724427664 8.95E-06 NA mr1181 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
vg0724427664 7.68E-07 NA mr1343 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
vg0724427664 8.25E-20 6.08E-15 mr1354 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
vg0724427664 1.01E-14 2.26E-11 mr1354 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
vg0724427664 2.14E-06 7.72E-06 mr1406 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
vg0724427664 NA 2.84E-08 mr1716 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
vg0724427664 2.77E-10 NA mr1829 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
vg0724427664 1.23E-09 2.10E-06 mr1829 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
vg0724427664 NA 2.78E-07 mr1915 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
vg0724427664 NA 3.99E-06 mr1977 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
vg0724427664 8.45E-09 NA mr1181_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
vg0724427664 1.84E-29 2.54E-16 mr1354_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
vg0724427664 1.33E-20 4.96E-11 mr1354_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
vg0724427664 NA 3.22E-06 mr1510_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
vg0724427664 5.01E-16 NA mr1829_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
vg0724427664 5.50E-11 1.02E-08 mr1829_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
vg0724427664 6.94E-16 NA mr1902_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
vg0724427664 6.13E-11 3.77E-08 mr1902_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