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Detailed information for vg0313902394:

Variant ID: vg0313902394 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 13902394
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: 291. )

Flanking Sequence (100 bp) in Reference Genome:


CCAGGTTTTGAGCAGTTTTCAATCATCTCACCTCTAATTCCTTCAATTTGCAATGGCTCCCCTCGTAATCCCCTCGTTGTCGTCAATTTCGTCCCTGGTA[C/T]
GTTCTCTCCATTTTTTGTTTGTTTGAGTAGCTGTTAAATAACACTCCAATCCAAAGTCTCCAATCATCCTAGAGGATAAGACTTCAAGTCTAATTTTGTT

Reverse complement sequence

AACAAAATTAGACTTGAAGTCTTATCCTCTAGGATGATTGGAGACTTTGGATTGGAGTGTTATTTAACAGCTACTCAAACAAACAAAAAATGGAGAGAAC[G/A]
TACCAGGGACGAAATTGACGACAACGAGGGGATTACGAGGGGAGCCATTGCAAATTGAAGGAATTAGAGGTGAGATGATTGAAAACTGCTCAAAACCTGG

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 97.30% 2.20% 0.49% 0.00% NA
All Indica  2759 100.00% 0.00% 0.04% 0.00% NA
All Japonica  1512 92.00% 6.70% 1.32% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.00% 0.13% 0.00% NA
Temperate Japonica  767 98.70% 0.90% 0.39% 0.00% NA
Tropical Japonica  504 81.00% 16.70% 2.38% 0.00% NA
Japonica Intermediate  241 93.80% 4.10% 2.07% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 95.60% 2.20% 2.22% 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
vg0313902394 C -> T LOC_Os03g24410.1 upstream_gene_variant ; 2315.0bp to feature; MODIFIER silent_mutation Average:58.881; most accessible tissue: Minghui63 panicle, score: 73.225 N N N N
vg0313902394 C -> T LOC_Os03g24400-LOC_Os03g24410 intergenic_region ; MODIFIER silent_mutation Average:58.881; most accessible tissue: Minghui63 panicle, score: 73.225 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0313902394 NA 2.38E-07 mr1951 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
vg0313902394 NA 2.25E-11 mr1055_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
vg0313902394 NA 2.03E-07 mr1232_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
vg0313902394 NA 1.08E-07 mr1261_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
vg0313902394 NA 1.97E-08 mr1401_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
vg0313902394 NA 3.52E-06 mr1415_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
vg0313902394 8.99E-06 8.99E-06 mr1424_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
vg0313902394 NA 5.84E-08 mr1557_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
vg0313902394 NA 6.62E-09 mr1558_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
vg0313902394 2.50E-07 2.50E-07 mr1562_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
vg0313902394 NA 2.34E-06 mr1849_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
vg0313902394 NA 3.50E-09 mr1905_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
vg0313902394 NA 5.08E-09 mr1942_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
vg0313902394 NA 8.80E-07 mr1944_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