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Detailed information for vg0128509483:

Variant ID: vg0128509483 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 28509483
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GATGGGAGGCGCGTGATGGTGGCGGTGTCTAGGCCGAACCTGGGCAGCGTCGGCTGCTGCTGCTCCTGCTCCATGACCAGTGGACGATCACGCCGGCGAC[A/G]
GGCAATGCGGAGGGCTCGAGGGCAGATGAAGATGGTGATGAGGAAGAAGCTTAGGGCGAACGACGCGGCCAAGGCACCGAACAACATCATGGTGCTGCAG

Reverse complement sequence

CTGCAGCACCATGATGTTGTTCGGTGCCTTGGCCGCGTCGTTCGCCCTAAGCTTCTTCCTCATCACCATCTTCATCTGCCCTCGAGCCCTCCGCATTGCC[T/C]
GTCGCCGGCGTGATCGTCCACTGGTCATGGAGCAGGAGCAGCAGCAGCCGACGCTGCCCAGGTTCGGCCTAGACACCGCCACCATCACGCGCCTCCCATC

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 25.00% 18.30% 4.36% 52.37% NA
All Indica  2759 1.60% 21.90% 6.60% 69.95% NA
All Japonica  1512 72.00% 16.10% 1.12% 10.71% NA
Aus  269 3.00% 0.00% 1.49% 95.54% NA
Indica I  595 2.00% 8.20% 5.38% 84.37% NA
Indica II  465 2.80% 12.90% 4.09% 80.22% NA
Indica III  913 0.40% 42.10% 9.64% 47.86% NA
Indica Intermediate  786 1.90% 14.00% 5.47% 78.63% NA
Temperate Japonica  767 92.70% 0.30% 0.00% 7.04% NA
Tropical Japonica  504 32.70% 44.60% 3.37% 19.25% NA
Japonica Intermediate  241 88.40% 7.10% 0.00% 4.56% NA
VI/Aromatic  96 13.50% 0.00% 2.08% 84.38% NA
Intermediate  90 31.10% 17.80% 1.11% 50.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0128509483 A -> G LOC_Os01g49570.1 missense_variant ; p.Cys31Arg; MODERATE nonsynonymous_codon ; C31R Average:30.621; most accessible tissue: Zhenshan97 panicle, score: 49.416 unknown unknown TOLERATED 1.00
vg0128509483 A -> DEL LOC_Os01g49570.1 N frameshift_variant Average:30.621; most accessible tissue: Zhenshan97 panicle, score: 49.416 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0128509483 NA 9.77E-06 mr1047 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
vg0128509483 NA 4.86E-07 mr1543 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
vg0128509483 NA 3.12E-06 mr1642 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
vg0128509483 NA 7.51E-07 mr1742 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
vg0128509483 NA 6.02E-06 mr1871 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
vg0128509483 NA 1.89E-06 mr1903 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
vg0128509483 NA 8.87E-06 mr1990 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
vg0128509483 NA 5.51E-08 mr1526_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
vg0128509483 NA 4.66E-51 mr1991_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