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Detailed information for vg0113026938:

Variant ID: vg0113026938 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 13026938
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:


CATCAAAGCAAATTCCTGGGCATGATATTTCGAACTTTCAATTAGCTTAACAGAAGATAAAAGCATACTTTTGAGGAAGGCTGAAATGTTTGAATACATA[C/A]
CGGTGGAGGAGGGTTGAAGGCGTTGTATGGCACCACTGGTAGCAAATGCGAATAGCTGACCATGATAGCGTTTGAGAAGATTTTGTACATTCTCTCCTTC

Reverse complement sequence

GAAGGAGAGAATGTACAAAATCTTCTCAAACGCTATCATGGTCAGCTATTCGCATTTGCTACCAGTGGTGCCATACAACGCCTTCAACCCTCCTCCACCG[G/T]
TATGTATTCAAACATTTCAGCCTTCCTCAAAAGTATGCTTTTATCTTCTGTTAAGCTAATTGAAAGTTCGAAATATCATGCCCAGGAATTTGCTTTGATG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 54.10% 4.30% 2.29% 39.25% NA
All Indica  2759 30.80% 7.20% 1.67% 60.35% NA
All Japonica  1512 96.80% 0.20% 1.19% 1.85% NA
Aus  269 32.30% 0.70% 14.13% 52.79% NA
Indica I  595 51.40% 1.00% 0.84% 46.72% NA
Indica II  465 41.90% 2.80% 1.51% 53.76% NA
Indica III  913 6.70% 15.10% 1.20% 77.00% NA
Indica Intermediate  786 36.60% 5.20% 2.93% 55.22% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 91.10% 0.40% 3.37% 5.16% NA
Japonica Intermediate  241 98.30% 0.40% 0.41% 0.83% NA
VI/Aromatic  96 89.60% 0.00% 2.08% 8.33% NA
Intermediate  90 80.00% 2.20% 4.44% 13.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0113026938 C -> A LOC_Os01g23180.1 N splice_donor_variant Average:9.08; most accessible tissue: Callus, score: 37.235 N N N N
vg0113026938 C -> DEL LOC_Os01g23180.1 N splice_donor_variant Average:9.08; most accessible tissue: Callus, score: 37.235 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0113026938 9.91E-08 5.53E-10 mr1238 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
vg0113026938 2.09E-06 9.85E-08 mr1309 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
vg0113026938 2.73E-08 1.80E-10 mr1841 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
vg0113026938 1.38E-07 1.38E-07 mr1900 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
vg0113026938 9.36E-07 2.10E-09 mr1238_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
vg0113026938 1.09E-06 6.64E-09 mr1484_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
vg0113026938 2.71E-07 2.11E-11 mr1841_2 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
vg0113026938 NA 4.63E-08 mr1900_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