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Detailed information for vg1012224057:

Variant ID: vg1012224057 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 12224057
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, A: 0.03, others allele: 0.00, population size: 62. )

Flanking Sequence (100 bp) in Reference Genome:


GGAGCGTGAGCAGGAGGCGGCTGCGCGCAAGGCCGGCAACGGCGGTGCGGAGCGCGAGCAGGATGTGGCCGTGCGCGAGAAGGCTGTTGAACGCTGGCCG[G/A]
TACGAGGCTTGCTGCGGCCGCTGGTCGCTGGGTCTCGCCGGTATACCTACATATCCATGATCCTGGGTCTCGCAATGCACGGCCGCGGCGAGGATGCCCT

Reverse complement sequence

AGGGCATCCTCGCCGCGGCCGTGCATTGCGAGACCCAGGATCATGGATATGTAGGTATACCGGCGAGACCCAGCGACCAGCGGCCGCAGCAAGCCTCGTA[C/T]
CGGCCAGCGTTCAACAGCCTTCTCGCGCACGGCCACATCCTGCTCGCGCTCCGCACCGCCGTTGCCGGCCTTGCGCGCAGCCGCCTCCTGCTCACGCTCC

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 31.30% 17.60% 1.18% 49.87% NA
All Indica  2759 2.70% 28.40% 1.81% 67.09% NA
All Japonica  1512 89.30% 0.40% 0.00% 10.32% NA
Aus  269 3.70% 9.30% 1.49% 85.50% NA
Indica I  595 4.00% 7.10% 2.86% 86.05% NA
Indica II  465 3.00% 35.90% 2.37% 58.71% NA
Indica III  913 1.30% 33.50% 1.20% 63.96% NA
Indica Intermediate  786 3.10% 34.20% 1.40% 61.32% NA
Temperate Japonica  767 97.00% 0.30% 0.00% 2.74% NA
Tropical Japonica  504 81.50% 0.40% 0.00% 18.06% NA
Japonica Intermediate  241 80.90% 0.80% 0.00% 18.26% NA
VI/Aromatic  96 6.20% 3.10% 1.04% 89.58% NA
Intermediate  90 43.30% 17.80% 1.11% 37.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1012224057 G -> A LOC_Os10g23830.1 missense_variant ; p.Val51Ile; MODERATE nonsynonymous_codon ; V51I Average:13.887; most accessible tissue: Callus, score: 51.074 unknown unknown TOLERATED 0.97
vg1012224057 G -> DEL LOC_Os10g23830.1 N frameshift_variant Average:13.887; most accessible tissue: Callus, score: 51.074 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1012224057 NA 5.05E-06 mr1157 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
vg1012224057 NA 9.21E-08 mr1328 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
vg1012224057 NA 1.93E-06 mr1415 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
vg1012224057 NA 1.42E-06 mr1420 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
vg1012224057 NA 6.62E-08 mr1446 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
vg1012224057 NA 1.93E-06 mr1567 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
vg1012224057 NA 8.42E-06 mr1689 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
vg1012224057 NA 3.30E-14 mr1909 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
vg1012224057 NA 1.96E-11 mr1921 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
vg1012224057 NA 8.26E-08 mr1158_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
vg1012224057 NA 4.98E-07 mr1369_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
vg1012224057 4.33E-06 2.08E-09 mr1446_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
vg1012224057 NA 1.12E-07 mr1453_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
vg1012224057 NA 1.75E-06 mr1467_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
vg1012224057 NA 4.59E-06 mr1556_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
vg1012224057 NA 1.96E-09 mr1567_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
vg1012224057 NA 6.39E-06 mr1567_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
vg1012224057 NA 7.10E-06 mr1633_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
vg1012224057 NA 5.75E-12 mr1641_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
vg1012224057 NA 2.79E-07 mr1706_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
vg1012224057 NA 6.27E-06 mr1764_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
vg1012224057 NA 3.77E-06 mr1811_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
vg1012224057 NA 1.34E-08 mr1921_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
vg1012224057 NA 4.94E-06 mr1951_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