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Detailed information for vg0404504944:

Variant ID: vg0404504944 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 4504944
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.71, T: 0.29, others allele: 0.00, population size: 58. )

Flanking Sequence (100 bp) in Reference Genome:


AACATGCAGACGTATATACTCTCTCCGTTTCGTTTTATTTGACACCGTTGACTTTTTAGCATATGTTTGACCGCTCGTCTTATTCAAAAAATTTAAATAA[T/C]
TATTAATTCTTTTGCTATCATTTGATTCATCGTTAAATATACTTTTATGCATACGTATAGTTTTACATATTTCACCAAAGTTTTTAATAAGACGAACGGT

Reverse complement sequence

ACCGTTCGTCTTATTAAAAACTTTGGTGAAATATGTAAAACTATACGTATGCATAAAAGTATATTTAACGATGAATCAAATGATAGCAAAAGAATTAATA[A/G]
TTATTTAAATTTTTTGAATAAGACGAGCGGTCAAACATATGCTAAAAAGTCAACGGTGTCAAATAAAACGAAACGGAGAGAGTATATACGTCTGCATGTT

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 45.20% 23.40% 7.53% 23.83% NA
All Indica  2759 53.90% 6.10% 11.16% 28.92% NA
All Japonica  1512 31.50% 60.40% 1.72% 6.42% NA
Aus  269 20.40% 3.00% 3.35% 73.23% NA
Indica I  595 63.20% 6.70% 14.29% 15.80% NA
Indica II  465 18.30% 4.90% 15.27% 61.51% NA
Indica III  913 72.20% 6.20% 5.37% 16.21% NA
Indica Intermediate  786 46.60% 6.00% 13.10% 34.35% NA
Temperate Japonica  767 9.50% 90.20% 0.13% 0.13% NA
Tropical Japonica  504 58.90% 19.20% 4.76% 17.06% NA
Japonica Intermediate  241 44.00% 51.50% 0.41% 4.15% NA
VI/Aromatic  96 87.50% 0.00% 4.17% 8.33% NA
Intermediate  90 41.10% 20.00% 10.00% 28.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0404504944 T -> C LOC_Os04g08400.1 downstream_gene_variant ; 1203.0bp to feature; MODIFIER silent_mutation Average:48.4; most accessible tissue: Minghui63 panicle, score: 74.563 N N N N
vg0404504944 T -> C LOC_Os04g08410.1 downstream_gene_variant ; 3860.0bp to feature; MODIFIER silent_mutation Average:48.4; most accessible tissue: Minghui63 panicle, score: 74.563 N N N N
vg0404504944 T -> C LOC_Os04g08400-LOC_Os04g08410 intergenic_region ; MODIFIER silent_mutation Average:48.4; most accessible tissue: Minghui63 panicle, score: 74.563 N N N N
vg0404504944 T -> DEL N N silent_mutation Average:48.4; most accessible tissue: Minghui63 panicle, score: 74.563 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0404504944 NA 6.40E-06 mr1164 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
vg0404504944 NA 7.23E-09 mr1194 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
vg0404504944 5.97E-06 NA mr1698 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
vg0404504944 NA 9.76E-06 mr1329_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
vg0404504944 1.13E-06 NA mr1549_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
vg0404504944 NA 4.19E-06 mr1566_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
vg0404504944 1.20E-06 NA mr1698_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
vg0404504944 NA 2.34E-06 mr1698_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
vg0404504944 NA 3.61E-06 mr1730_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
vg0404504944 NA 2.15E-07 mr1743_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
vg0404504944 3.54E-07 NA mr1757_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
vg0404504944 NA 4.30E-11 mr1851_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
vg0404504944 NA 2.38E-07 mr1860_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
vg0404504944 NA 1.58E-07 mr1866_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
vg0404504944 NA 1.87E-09 mr1905_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