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Detailed information for vg1013484683:

Variant ID: vg1013484683 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 13484683
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.65, G: 0.35, others allele: 0.00, population size: 204. )

Flanking Sequence (100 bp) in Reference Genome:


GTAGAACCAATTGGTGTTGAAATTGGCTTGCAATTCTCCATCTTGAACCGTTCCAAAAGATCCTTCGTATACTTGGTTTGATGCACAAAAGTACCTTGAG[G/A]
TGTTTGCTTAATTTGCAATCCCAAAAAGTATGATAACTCACCCATCATGCTCATCTCAAATTCCCTGCGCATATTCTCAGCAAAATCTACAACCAAAGCG

Reverse complement sequence

CGCTTTGGTTGTAGATTTTGCTGAGAATATGCGCAGGGAATTTGAGATGAGCATGATGGGTGAGTTATCATACTTTTTGGGATTGCAAATTAAGCAAACA[C/T]
CTCAAGGTACTTTTGTGCATCAAACCAAGTATACGAAGGATCTTTTGGAACGGTTCAAGATGGAGAATTGCAAGCCAATTTCAACACCAATTGGTTCTAC

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 75.10% 24.80% 0.17% 0.00% NA
All Indica  2759 98.70% 1.10% 0.18% 0.00% NA
All Japonica  1512 32.20% 67.80% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.50% 0.00% 0.50% 0.00% NA
Indica II  465 96.60% 3.20% 0.22% 0.00% NA
Indica III  913 99.70% 0.30% 0.00% 0.00% NA
Indica Intermediate  786 98.20% 1.70% 0.13% 0.00% NA
Temperate Japonica  767 5.70% 94.30% 0.00% 0.00% NA
Tropical Japonica  504 65.70% 34.30% 0.00% 0.00% NA
Japonica Intermediate  241 46.50% 53.50% 0.00% 0.00% NA
VI/Aromatic  96 19.80% 80.20% 0.00% 0.00% NA
Intermediate  90 55.60% 41.10% 3.33% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1013484683 G -> A LOC_Os10g26040.1 missense_variant ; p.Pro1040Ser; MODERATE nonsynonymous_codon ; P1040S Average:15.899; most accessible tissue: Minghui63 young leaf, score: 23.613 benign 0.363 TOLERATED 0.26

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1013484683 NA 1.53E-15 mr1301 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
vg1013484683 NA 9.19E-12 mr1410 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
vg1013484683 NA 4.74E-06 mr1424 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
vg1013484683 1.91E-10 4.88E-19 mr1533 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
vg1013484683 4.47E-08 1.63E-21 mr1980 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
vg1013484683 NA 1.83E-12 mr1410_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
vg1013484683 4.73E-15 7.93E-31 mr1533_2 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
vg1013484683 NA 1.45E-07 mr1578_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
vg1013484683 NA 2.18E-18 mr1980_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
vg1013484683 3.02E-07 1.33E-12 mr1980_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