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Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0124008913:

Variant ID: vg0124008913 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 24008913
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.90, A: 0.10, others allele: 0.00, population size: 92. )

Flanking Sequence (100 bp) in Reference Genome:


CGAGGCAACGCCAAGTCCTCTCTTGCAATGTCACAAATCACCAAACTCAGCAAGAAGTTGACATAGTACGTACTCCCTCCGTATTCGTATTTTAATTTAT[G/A]
ACGCCGTTGACTTTTTATCAATTTTTATCCTTCGTTTTATTTAAAATTTTTATGTAAATATGAAAATATTTATATCATACTTAAAGAATATTTGATGATG

Reverse complement sequence

CATCATCAAATATTCTTTAAGTATGATATAAATATTTTCATATTTACATAAAAATTTTAAATAAAACGAAGGATAAAAATTGATAAAAAGTCAACGGCGT[C/T]
ATAAATTAAAATACGAATACGGAGGGAGTACGTACTATGTCAACTTCTTGCTGAGTTTGGTGATTTGTGACATTGCAAGAGAGGACTTGGCGTTGCCTCG

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 53.70% 41.80% 0.11% 4.38% NA
All Indica  2759 33.80% 65.80% 0.11% 0.29% NA
All Japonica  1512 78.40% 8.50% 0.13% 12.90% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 61.20% 38.70% 0.17% 0.00% NA
Indica II  465 12.90% 86.50% 0.00% 0.65% NA
Indica III  913 29.90% 69.90% 0.11% 0.11% NA
Indica Intermediate  786 30.00% 69.30% 0.13% 0.51% NA
Temperate Japonica  767 87.40% 12.10% 0.13% 0.39% NA
Tropical Japonica  504 59.10% 5.60% 0.00% 35.32% NA
Japonica Intermediate  241 90.50% 3.30% 0.41% 5.81% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 62.20% 33.30% 0.00% 4.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0124008913 G -> A LOC_Os01g42310-LOC_Os01g42320 intergenic_region ; MODIFIER silent_mutation Average:44.674; most accessible tissue: Zhenshan97 root, score: 82.361 N N N N
vg0124008913 G -> DEL N N silent_mutation Average:44.674; most accessible tissue: Zhenshan97 root, score: 82.361 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0124008913 NA 2.35E-07 mr1028 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
vg0124008913 1.27E-06 1.27E-06 mr1369 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
vg0124008913 NA 4.08E-07 mr1453 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
vg0124008913 NA 1.27E-08 mr1652 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
vg0124008913 NA 9.52E-06 mr1318_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
vg0124008913 NA 1.59E-06 mr1510_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
vg0124008913 NA 1.09E-06 mr1528_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
vg0124008913 NA 3.13E-06 mr1702_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
vg0124008913 NA 1.40E-09 mr1758_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
vg0124008913 NA 3.33E-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
vg0124008913 NA 2.10E-06 mr1842_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