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Detailed information for vg1000929697:

Variant ID: vg1000929697 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 929697
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CGGTGAGGTTGGGGTAACACGCCAGAAAGCCGTCGGGAAGCCGGCCGGCGAGGCCGCCATCGGAGAGGTCGAGCTGCAGCAGCGCGCGCGGGAGCTTAAC[C/T]
AGGTCACCGGCATCAACGTGCAGCTCGCCATTGCCGGAGAGGTTCAACCTGCACAACGTGTCGAGACCAGAGAGGGCGGCAAGCTCGGCGCGCCCGGCGA

Reverse complement sequence

TCGCCGGGCGCGCCGAGCTTGCCGCCCTCTCTGGTCTCGACACGTTGTGCAGGTTGAACCTCTCCGGCAATGGCGAGCTGCACGTTGATGCCGGTGACCT[G/A]
GTTAAGCTCCCGCGCGCGCTGCTGCAGCTCGACCTCTCCGATGGCGGCCTCGCCGGCCGGCTTCCCGACGGCTTTCTGGCGTGTTACCCCAACCTCACCG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 96.60% 2.50% 0.95% 0.00% NA
All Indica  2759 99.70% 0.20% 0.07% 0.00% NA
All Japonica  1512 89.90% 7.30% 2.71% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.20% 0.50% 0.25% 0.00% NA
Temperate Japonica  767 98.30% 0.00% 1.69% 0.00% NA
Tropical Japonica  504 75.80% 20.00% 4.17% 0.00% NA
Japonica Intermediate  241 92.90% 4.10% 2.90% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 95.60% 2.20% 2.22% 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
vg1000929697 C -> T LOC_Os10g02500.1 synonymous_variant ; p.Leu108Leu; LOW synonymous_codon Average:80.543; most accessible tissue: Zhenshan97 young leaf, score: 85.364 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1000929697 2.90E-06 2.90E-06 mr1058 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
vg1000929697 5.15E-06 NA mr1084 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
vg1000929697 NA 2.30E-06 mr1218 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
vg1000929697 NA 9.38E-06 mr1345 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
vg1000929697 NA 5.21E-06 mr1414 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
vg1000929697 NA 1.87E-06 mr1602 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
vg1000929697 NA 1.78E-07 mr1638 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
vg1000929697 NA 1.20E-07 mr1696 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
vg1000929697 1.04E-06 NA mr1754 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