Search for Variation information by Variation ID:

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

Detailed information for vg0515312990:

Variant ID: vg0515312990 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 15312990
Reference Allele: AAlternative Allele: T,G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.81, G: 0.19, others allele: 0.00, population size: 69. )

Flanking Sequence (100 bp) in Reference Genome:


CCCTGGATAGGGATTGGTGTAGTGGATCCTTTGGTTAGCCCCCTGTTGGTGGCGGAAATTCGCCAGGCGATGCTTGTGCGACTCCAGTTCCTTGTGCTTG[A/T,G]
CTTCCAAGCGGATGCTCTTGTCCACCAGACGTTGGAAATCCGGAGAGTCCCCGGAGACTAGACGCACGGACAGCTCAGGGTCCATTCCTGCCAAGAACTT

Reverse complement sequence

AAGTTCTTGGCAGGAATGGACCCTGAGCTGTCCGTGCGTCTAGTCTCCGGGGACTCTCCGGATTTCCAACGTCTGGTGGACAAGAGCATCCGCTTGGAAG[T/A,C]
CAAGCACAAGGAACTGGAGTCGCACAAGCATCGCCTGGCGAATTTCCGCCACCAACAGGGGGCTAACCAAAGGATCCACTACACCAATCCCTATCCAGGG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 46.20% 25.90% 5.27% 22.56% T: 0.13%
All Indica  2759 30.10% 29.10% 8.08% 32.48% T: 0.22%
All Japonica  1512 78.30% 11.20% 0.99% 9.46% NA
Aus  269 8.60% 83.30% 1.49% 6.69% NA
Indica I  595 25.20% 13.10% 7.73% 53.95% NA
Indica II  465 38.30% 27.30% 7.31% 27.10% NA
Indica III  913 34.70% 37.60% 8.54% 18.62% T: 0.55%
Indica Intermediate  786 23.50% 32.60% 8.27% 35.50% T: 0.13%
Temperate Japonica  767 94.30% 1.60% 0.13% 4.04% NA
Tropical Japonica  504 53.00% 27.60% 1.98% 17.46% NA
Japonica Intermediate  241 80.50% 7.90% 1.66% 9.96% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 56.70% 25.60% 7.78% 10.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0515312990 A -> T LOC_Os05g26320.1 missense_variant ; p.Val261Asp; MODERATE nonsynonymous_codon ; V261D Average:33.82; most accessible tissue: Zhenshan97 flag leaf, score: 60.705 unknown unknown TOLERATED 0.47
vg0515312990 A -> G LOC_Os05g26320.1 missense_variant ; p.Val261Ala; MODERATE nonsynonymous_codon ; V261A Average:33.82; most accessible tissue: Zhenshan97 flag leaf, score: 60.705 unknown unknown TOLERATED 1.00
vg0515312990 A -> DEL LOC_Os05g26320.1 N frameshift_variant Average:33.82; most accessible tissue: Zhenshan97 flag leaf, score: 60.705 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0515312990 NA 1.62E-17 mr1133 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
vg0515312990 NA 2.61E-08 mr1206 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
vg0515312990 NA 6.01E-08 mr1229 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
vg0515312990 NA 6.46E-08 mr1243 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
vg0515312990 NA 4.68E-09 mr1399 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
vg0515312990 NA 1.34E-06 mr1596 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
vg0515312990 1.57E-06 5.63E-21 mr1699 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
vg0515312990 NA 6.35E-08 mr1800 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
vg0515312990 NA 2.77E-08 mr1862 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
vg0515312990 NA 1.14E-06 mr1039_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
vg0515312990 NA 1.31E-07 mr1217_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
vg0515312990 NA 1.98E-11 mr1410_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
vg0515312990 NA 7.97E-08 mr1551_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
vg0515312990 NA 2.82E-07 mr1632_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
vg0515312990 NA 2.42E-07 mr1676_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
vg0515312990 NA 1.40E-07 mr1696_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
vg0515312990 NA 2.60E-06 mr1873_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
vg0515312990 NA 5.48E-10 mr1916_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