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Detailed information for vg0800293632:

Variant ID: vg0800293632 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 293632
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.92, T: 0.08, others allele: 0.00, population size: 204. )

Flanking Sequence (100 bp) in Reference Genome:


CGAAGTTTATACCTGGGCATATCCTTCGACCAGTCCTGAATGGCAAGAAATTGAAATTATTTCCATTGTAGTCAGCCATTGTGTTGCTAAGGAACCTCTC[T/C]
GGCATGAACTCCTCGGCATTTTCCCAATAGCTAGGGTCCCTGGCAATAGCCCATGCATTGACGATGACACGAGTGCCTGAGGGTATAGTATAGCCCTCGA

Reverse complement sequence

TCGAGGGCTATACTATACCCTCAGGCACTCGTGTCATCGTCAATGCATGGGCTATTGCCAGGGACCCTAGCTATTGGGAAAATGCCGAGGAGTTCATGCC[A/G]
GAGAGGTTCCTTAGCAACACAATGGCTGACTACAATGGAAATAATTTCAATTTCTTGCCATTCAGGACTGGTCGAAGGATATGCCCAGGTATAAACTTCG

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 59.20% 40.30% 0.19% 0.28% NA
All Indica  2759 38.40% 60.80% 0.33% 0.43% NA
All Japonica  1512 98.40% 1.60% 0.00% 0.00% NA
Aus  269 37.90% 62.10% 0.00% 0.00% NA
Indica I  595 31.80% 67.60% 0.34% 0.34% NA
Indica II  465 14.80% 84.10% 0.43% 0.65% NA
Indica III  913 58.80% 40.50% 0.33% 0.33% NA
Indica Intermediate  786 33.70% 65.50% 0.25% 0.51% NA
Temperate Japonica  767 98.60% 1.40% 0.00% 0.00% NA
Tropical Japonica  504 98.20% 1.80% 0.00% 0.00% NA
Japonica Intermediate  241 98.30% 1.70% 0.00% 0.00% NA
VI/Aromatic  96 93.80% 6.20% 0.00% 0.00% NA
Intermediate  90 65.60% 33.30% 0.00% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0800293632 T -> C LOC_Os08g01470.1 synonymous_variant ; p.Pro256Pro; LOW synonymous_codon Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0800293632 T -> DEL LOC_Os08g01470.1 N frameshift_variant Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0800293632 NA 2.97E-06 mr1195 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
vg0800293632 7.24E-07 NA mr1277 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
vg0800293632 2.06E-08 1.45E-11 mr1277 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
vg0800293632 1.02E-11 NA mr1746 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
vg0800293632 4.76E-14 1.08E-17 mr1746 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
vg0800293632 NA 4.86E-12 mr1751 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
vg0800293632 6.58E-08 NA mr1277_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
vg0800293632 8.17E-09 4.97E-11 mr1277_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
vg0800293632 1.54E-07 3.61E-09 mr1403_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
vg0800293632 8.05E-15 NA mr1746_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
vg0800293632 3.49E-16 1.13E-21 mr1746_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