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Detailed information for vg0908235271:

Variant ID: vg0908235271 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 8235271
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.02, others allele: 0.00, population size: 59. )

Flanking Sequence (100 bp) in Reference Genome:


CGATCAGGCTATCATCAGTTGAGAATTCAGGAGGAGGATATTCCCAAGACAGCCTTCACCACTCGGTATGGGTTGTTTGAGTGCACGGTTATGTCATTTG[G/A]
ACTCACCAATGCACCGGTTTTCTTCATGAACTTGATGAACAAAGTGTTTATGGAATTTCTGGACAAGTTTGTCGTGGTGTTCATTGACGACATACTTATT

Reverse complement sequence

AATAAGTATGTCGTCAATGAACACCACGACAAACTTGTCCAGAAATTCCATAAACACTTTGTTCATCAAGTTCATGAAGAAAACCGGTGCATTGGTGAGT[C/T]
CAAATGACATAACCGTGCACTCAAACAACCCATACCGAGTGGTGAAGGCTGTCTTGGGAATATCCTCCTCCTGAATTCTCAACTGATGATAGCCTGATCG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 92.50% 0.90% 5.04% 1.59% NA
All Indica  2759 93.30% 1.60% 5.18% 0.00% NA
All Japonica  1512 88.90% 0.00% 6.15% 4.96% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 89.20% 3.00% 7.73% 0.00% NA
Indica II  465 94.60% 1.10% 4.30% 0.00% NA
Indica III  913 96.90% 0.10% 2.96% 0.00% NA
Indica Intermediate  786 91.20% 2.40% 6.36% 0.00% NA
Temperate Japonica  767 96.30% 0.00% 1.43% 2.22% NA
Tropical Japonica  504 84.70% 0.00% 12.30% 2.98% NA
Japonica Intermediate  241 73.90% 0.00% 8.30% 17.84% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 97.80% 0.00% 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
vg0908235271 G -> DEL LOC_Os09g13980.1 N frameshift_variant Average:23.874; most accessible tissue: Minghui63 young leaf, score: 61.007 N N N N
vg0908235271 G -> A LOC_Os09g13980.1 missense_variant ; p.Gly224Glu; MODERATE nonsynonymous_codon ; G224E Average:23.874; most accessible tissue: Minghui63 young leaf, score: 61.007 benign 0.908 DELETERIOUS 0.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0908235271 NA 2.46E-07 mr1089 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
vg0908235271 NA 8.91E-13 mr1109 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
vg0908235271 NA 9.91E-10 mr1129 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
vg0908235271 3.77E-07 NA mr1251 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
vg0908235271 6.55E-07 6.31E-11 mr1251 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
vg0908235271 NA 6.29E-07 mr1253 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
vg0908235271 NA 7.30E-18 mr1255 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
vg0908235271 NA 1.52E-08 mr1255 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
vg0908235271 NA 3.51E-09 mr1257 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
vg0908235271 NA 9.69E-07 mr1423 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
vg0908235271 NA 1.59E-08 mr1435 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
vg0908235271 NA 1.18E-06 mr1599 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
vg0908235271 NA 2.65E-12 mr1109_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
vg0908235271 NA 2.45E-10 mr1129_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
vg0908235271 NA 2.36E-08 mr1236_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
vg0908235271 NA 2.61E-08 mr1236_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
vg0908235271 NA 5.36E-07 mr1255_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
vg0908235271 NA 1.18E-09 mr1257_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
vg0908235271 NA 2.15E-06 mr1863_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