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Detailed information for vg1124292282:

Variant ID: vg1124292282 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 24292282
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:


TAATCATGGACTAATTAGGCTCAAAAGATTCGCCTCGCAATTTACATGTAAATTGTGCAATTAATTTTTTTATTTTATCTATATTTAATGTTCCATGCAT[G/A]
CATGTGTCCATAGATTCGATGTGACGTTTTTGGGAAAAAAATTAGGAACAGCCTTAATTACACACTCACATAATATAGCATTATAGTCCTCGAAAGTTGG

Reverse complement sequence

CCAACTTTCGAGGACTATAATGCTATATTATGTGAGTGTGTAATTAAGGCTGTTCCTAATTTTTTTCCCAAAAACGTCACATCGAATCTATGGACACATG[C/T]
ATGCATGGAACATTAAATATAGATAAAATAAAAAAATTAATTGCACAATTTACATGTAAATTGCGAGGCGAATCTTTTGAGCCTAATTAGTCCATGATTA

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 56.80% 38.20% 0.17% 4.80% NA
All Indica  2759 49.40% 49.80% 0.22% 0.62% NA
All Japonica  1512 74.30% 13.70% 0.07% 11.90% NA
Aus  269 31.60% 60.60% 0.00% 7.81% NA
Indica I  595 21.80% 77.80% 0.34% 0.00% NA
Indica II  465 42.80% 56.10% 0.43% 0.65% NA
Indica III  913 72.20% 26.90% 0.11% 0.77% NA
Indica Intermediate  786 47.60% 51.40% 0.13% 0.89% NA
Temperate Japonica  767 87.50% 8.10% 0.13% 4.30% NA
Tropical Japonica  504 67.90% 10.30% 0.00% 21.83% NA
Japonica Intermediate  241 46.10% 38.60% 0.00% 15.35% NA
VI/Aromatic  96 75.00% 24.00% 0.00% 1.04% NA
Intermediate  90 45.60% 44.40% 1.11% 8.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1124292282 G -> A LOC_Os11g40680-LOC_Os11g40690 intergenic_region ; MODIFIER silent_mutation Average:38.82; most accessible tissue: Zhenshan97 young leaf, score: 55.899 N N N N
vg1124292282 G -> DEL N N silent_mutation Average:38.82; most accessible tissue: Zhenshan97 young leaf, score: 55.899 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1124292282 NA 8.60E-08 mr1133 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
vg1124292282 NA 2.89E-06 mr1180 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
vg1124292282 NA 3.66E-06 mr1183 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
vg1124292282 NA 4.75E-08 mr1280 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
vg1124292282 NA 3.97E-06 mr1503 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
vg1124292282 NA 3.23E-07 mr1729 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
vg1124292282 NA 5.96E-07 mr1788 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
vg1124292282 NA 1.01E-08 mr1807 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
vg1124292282 NA 6.58E-07 mr1183_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
vg1124292282 NA 2.09E-07 mr1528_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
vg1124292282 NA 9.33E-07 mr1788_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
vg1124292282 NA 1.88E-06 mr1788_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