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Detailed information for vg0414211322:

Variant ID: vg0414211322 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 14211322
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.87, T: 0.13, others allele: 0.00, population size: 105. )

Flanking Sequence (100 bp) in Reference Genome:


GAGGCTAAATATTCACTGTCGATAACAATCAATGCTTAACTAGTCCTTTAAAAAAACTTAAAATTTAGCTCTTTAACAATAATAATCACTACTAGAAAAA[T/C]
AATTTTTCATGACGTCACACTATAATTTTCACTGGCGGTTATATGCTAAAACTACTAGCAAAAACATAAGCAGAGGTTGGGGGTATAGGACCACCAGCGA

Reverse complement sequence

TCGCTGGTGGTCCTATACCCCCAACCTCTGCTTATGTTTTTGCTAGTAGTTTTAGCATATAACCGCCAGTGAAAATTATAGTGTGACGTCATGAAAAATT[A/G]
TTTTTCTAGTAGTGATTATTATTGTTAAAGAGCTAAATTTTAAGTTTTTTTAAAGGACTAGTTAAGCATTGATTGTTATCGACAGTGAATATTTAGCCTC

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 63.90% 36.10% 0.02% 0.00% NA
All Indica  2759 85.40% 14.60% 0.00% 0.00% NA
All Japonica  1512 18.40% 81.60% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 65.70% 34.30% 0.00% 0.00% NA
Indica II  465 78.50% 21.50% 0.00% 0.00% NA
Indica III  913 97.60% 2.40% 0.00% 0.00% NA
Indica Intermediate  786 90.10% 9.90% 0.00% 0.00% NA
Temperate Japonica  767 5.60% 94.40% 0.00% 0.00% NA
Tropical Japonica  504 23.20% 76.80% 0.00% 0.00% NA
Japonica Intermediate  241 49.00% 51.00% 0.00% 0.00% NA
VI/Aromatic  96 64.60% 35.40% 0.00% 0.00% NA
Intermediate  90 63.30% 35.60% 1.11% 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
vg0414211322 T -> C LOC_Os04g24750.1 downstream_gene_variant ; 554.0bp to feature; MODIFIER silent_mutation Average:58.619; most accessible tissue: Zhenshan97 panicle, score: 76.605 N N N N
vg0414211322 T -> C LOC_Os04g24750-LOC_Os04g24770 intergenic_region ; MODIFIER silent_mutation Average:58.619; most accessible tissue: Zhenshan97 panicle, score: 76.605 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0414211322 NA 8.30E-06 mr1010 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
vg0414211322 NA 1.43E-06 mr1180 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
vg0414211322 NA 3.54E-06 mr1183 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
vg0414211322 NA 8.74E-09 mr1280 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
vg0414211322 NA 2.21E-06 mr1380 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
vg0414211322 NA 7.97E-06 mr1403 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
vg0414211322 NA 7.49E-06 mr1503 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
vg0414211322 1.55E-08 3.84E-12 mr1729 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
vg0414211322 NA 3.21E-08 mr1788 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
vg0414211322 NA 4.24E-11 mr1846 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
vg0414211322 NA 9.23E-07 mr1937 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
vg0414211322 NA 1.15E-06 mr1977_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