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Detailed information for vg0825194810:

Variant ID: vg0825194810 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 25194810
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.52, T: 0.48, others allele: 0.00, population size: 105. )

Flanking Sequence (100 bp) in Reference Genome:


TCTTCTGGGTCGGTGCTCCCATCGTACTTTTCTATTGCTCCAAGTCGGAATCTCTCAGGCCATCGGACATCACGCAGGGAACGACTGAAAGCTCTACACC[T/C]
AGCGCTGGGGACGGTGGGTTGTCGGCGATCGTGTGTCCTTCGTGGATGTCTGTCTGATGATGAAGAAGACGAGGATGATGACGATGATGATGGGTCGCTC

Reverse complement sequence

GAGCGACCCATCATCATCGTCATCATCCTCGTCTTCTTCATCATCAGACAGACATCCACGAAGGACACACGATCGCCGACAACCCACCGTCCCCAGCGCT[A/G]
GGTGTAGAGCTTTCAGTCGTTCCCTGCGTGATGTCCGATGGCCTGAGAGATTCCGACTTGGAGCAATAGAAAAGTACGATGGGAGCACCGACCCAGAAGA

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 68.70% 31.00% 0.19% 0.17% NA
All Indica  2759 56.60% 42.90% 0.25% 0.25% NA
All Japonica  1512 99.50% 0.50% 0.00% 0.00% NA
Aus  269 6.70% 93.30% 0.00% 0.00% NA
Indica I  595 65.40% 33.90% 0.34% 0.34% NA
Indica II  465 75.90% 23.70% 0.22% 0.22% NA
Indica III  913 39.30% 60.50% 0.11% 0.11% NA
Indica Intermediate  786 58.70% 40.60% 0.38% 0.38% NA
Temperate Japonica  767 99.50% 0.50% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 93.80% 6.20% 0.00% 0.00% NA
Intermediate  90 77.80% 18.90% 2.22% 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
vg0825194810 T -> C LOC_Os08g39810.1 missense_variant ; p.Arg953Gly; MODERATE nonsynonymous_codon ; R953G Average:46.522; most accessible tissue: Minghui63 panicle, score: 66.554 unknown unknown TOLERATED 1.00
vg0825194810 T -> DEL LOC_Os08g39810.1 N frameshift_variant Average:46.522; most accessible tissue: Minghui63 panicle, score: 66.554 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0825194810 NA 1.10E-07 mr1545 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
vg0825194810 3.50E-06 NA mr1699 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
vg0825194810 NA 1.42E-06 mr1699 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
vg0825194810 7.87E-17 1.70E-40 mr1874 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
vg0825194810 4.94E-19 7.92E-26 mr1874 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
vg0825194810 NA 1.40E-07 mr1004_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
vg0825194810 NA 6.11E-17 mr1587_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
vg0825194810 5.21E-08 NA mr1699_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
vg0825194810 3.82E-07 9.11E-10 mr1699_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
vg0825194810 2.91E-17 9.50E-59 mr1874_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
vg0825194810 2.28E-16 2.46E-30 mr1874_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