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Detailed information for vg1003073690:

Variant ID: vg1003073690 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 3073690
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 295. )

Flanking Sequence (100 bp) in Reference Genome:


TGGCCGAGAAACAACCACCACCACCATCTAGCCCAGGCTTTGTTAAGGACAAGATGCTAAAGCTAGGATTGACTGACGTCAATGAAGGAAACGTCGTGCC[G/A]
ATCGATCCAGAAAAATTCACACCTGAGCAGAAGAAAGAGTTTGAAGCAATGTTGCAGCAAGTACGGGATTAGTTCTTGAACTCATTCATGTAGACCCGCA

Reverse complement sequence

TGCGGGTCTACATGAATGAGTTCAAGAACTAATCCCGTACTTGCTGCAACATTGCTTCAAACTCTTTCTTCTGCTCAGGTGTGAATTTTTCTGGATCGAT[C/T]
GGCACGACGTTTCCTTCATTGACGTCAGTCAATCCTAGCTTTAGCATCTTGTCCTTAACAAAGCCTGGGCTAGATGGTGGTGGTGGTTGTTTCTCGGCCA

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 90.40% 9.10% 0.51% 0.00% NA
All Indica  2759 85.00% 14.80% 0.18% 0.00% NA
All Japonica  1512 97.50% 1.30% 1.19% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 82.00% 17.60% 0.34% 0.00% NA
Indica II  465 87.10% 12.70% 0.22% 0.00% NA
Indica III  913 85.10% 14.70% 0.22% 0.00% NA
Indica Intermediate  786 86.00% 14.00% 0.00% 0.00% NA
Temperate Japonica  767 95.00% 2.60% 2.35% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 95.60% 3.30% 1.11% 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
vg1003073690 G -> A LOC_Os10g06050.1 synonymous_variant ; p.Pro34Pro; LOW synonymous_codon Average:26.592; most accessible tissue: Minghui63 young leaf, score: 35.334 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1003073690 1.33E-06 NA mr1538 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
vg1003073690 1.01E-06 2.28E-08 mr1538 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
vg1003073690 4.86E-12 5.12E-12 mr1547 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
vg1003073690 9.42E-09 1.72E-10 mr1547 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
vg1003073690 2.62E-10 2.20E-12 mr1709 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
vg1003073690 8.54E-10 9.51E-11 mr1709 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
vg1003073690 NA 5.75E-08 mr1538_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
vg1003073690 2.16E-09 1.12E-11 mr1547_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
vg1003073690 5.70E-09 1.72E-12 mr1547_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
vg1003073690 9.77E-11 3.08E-13 mr1709_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
vg1003073690 1.29E-09 5.30E-11 mr1709_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