Search for Variation information by Variation ID:

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

Detailed information for vg0404659256:

Variant ID: vg0404659256 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 4659256
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:


CACCATCAGTGTCGTACAACTGCTAACACTTTACCCCTGCTGAGGACGTCCTTTGCCTCCAGCCTCCTTCTTCGGCATCAACGTCACCCACCTTCTCCGG[T/C]
GCCGCTCACCCCATCACCTACTGTCCAAGCGTCGCTGCTCCCCAACCTTATTTGCCTTCCTCTTTCTCTCATTCCAAGGTCACTTAAATTCCTAGGTATT

Reverse complement sequence

AATACCTAGGAATTTAAGTGACCTTGGAATGAGAGAAAGAGGAAGGCAAATAAGGTTGGGGAGCAGCGACGCTTGGACAGTAGGTGATGGGGTGAGCGGC[A/G]
CCGGAGAAGGTGGGTGACGTTGATGCCGAAGAAGGAGGCTGGAGGCAAAGGACGTCCTCAGCAGGGGTAAAGTGTTAGCAGTTGTACGACACTGATGGTG

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 75.70% 24.10% 0.13% 0.00% NA
All Indica  2759 93.60% 6.40% 0.00% 0.00% NA
All Japonica  1512 40.90% 58.70% 0.40% 0.00% NA
Aus  269 98.90% 1.10% 0.00% 0.00% NA
Indica I  595 98.20% 1.80% 0.00% 0.00% NA
Indica II  465 86.90% 13.10% 0.00% 0.00% NA
Indica III  913 96.70% 3.30% 0.00% 0.00% NA
Indica Intermediate  786 90.50% 9.50% 0.00% 0.00% NA
Temperate Japonica  767 12.40% 87.60% 0.00% 0.00% NA
Tropical Japonica  504 77.00% 21.80% 1.19% 0.00% NA
Japonica Intermediate  241 56.00% 44.00% 0.00% 0.00% NA
VI/Aromatic  96 46.90% 53.10% 0.00% 0.00% NA
Intermediate  90 75.60% 24.40% 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
vg0404659256 T -> C LOC_Os04g08570-LOC_Os04g08580 intergenic_region ; MODIFIER silent_mutation Average:58.18; most accessible tissue: Zhenshan97 young leaf, score: 88.259 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0404659256 NA 4.54E-10 mr1023_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
vg0404659256 5.57E-07 1.09E-15 mr1178_2 Ind_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
vg0404659256 NA 5.33E-08 mr1399_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
vg0404659256 NA 7.93E-09 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