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Detailed information for vg0408294799:

Variant ID: vg0408294799 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 8294799
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 112. )

Flanking Sequence (100 bp) in Reference Genome:


CAGGATGTGCCAGCCTCACACACGCAAGGACATGGCACACCCCGGTATAGATCCCGTTGAACGTCTCCTCTCCGACCCTGGCCGCGTGCTTGGAGGGGAT[C/T]
GCCTCCATCGCCGTTGCCAGTTCCGCAAGCGAAGACGTCAACGAGAACTCGTCGGGATTCGCCGGGATGGTGGCCTTGACGCCACACTCCCCGGCGAGCT

Reverse complement sequence

AGCTCGCCGGGGAGTGTGGCGTCAAGGCCACCATCCCGGCGAATCCCGACGAGTTCTCGTTGACGTCTTCGCTTGCGGAACTGGCAACGGCGATGGAGGC[G/A]
ATCCCCTCCAAGCACGCGGCCAGGGTCGGAGAGGAGACGTTCAACGGGATCTATACCGGGGTGTGCCATGTCCTTGCGTGTGTGAGGCTGGCACATCCTG

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 22.20% 15.30% 3.58% 58.89% NA
All Indica  2759 3.30% 6.80% 4.10% 85.83% NA
All Japonica  1512 61.80% 24.10% 1.46% 12.57% NA
Aus  269 1.90% 32.30% 7.43% 58.36% NA
Indica I  595 2.40% 0.70% 3.19% 93.78% NA
Indica II  465 3.20% 25.60% 4.73% 66.45% NA
Indica III  913 3.80% 2.20% 4.27% 89.70% NA
Indica Intermediate  786 3.40% 5.60% 4.20% 86.77% NA
Temperate Japonica  767 95.80% 1.20% 0.26% 2.74% NA
Tropical Japonica  504 6.50% 65.30% 3.37% 24.80% NA
Japonica Intermediate  241 69.30% 11.20% 1.24% 18.26% NA
VI/Aromatic  96 1.00% 59.40% 6.25% 33.33% NA
Intermediate  90 20.00% 31.10% 8.89% 40.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0408294799 C -> DEL LOC_Os04g14780.1 N frameshift_variant Average:17.471; most accessible tissue: Minghui63 root, score: 43.505 N N N N
vg0408294799 C -> T LOC_Os04g14780.1 synonymous_variant ; p.Ala280Ala; LOW synonymous_codon Average:17.471; most accessible tissue: Minghui63 root, score: 43.505 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0408294799 5.92E-06 NA mr1019 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
vg0408294799 1.41E-06 NA mr1023_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
vg0408294799 9.55E-06 NA mr1079_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
vg0408294799 3.17E-07 NA mr1132_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
vg0408294799 4.35E-06 NA mr1261_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
vg0408294799 1.24E-06 NA mr1390_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
vg0408294799 6.80E-06 NA mr1489_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
vg0408294799 1.68E-06 NA mr1490_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