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Detailed information for vg1014419290:

Variant ID: vg1014419290 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 14419290
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GAAACTCTTAGGGGTCTTCCAGCTAGCTCCACAAGCTAGTGGGCTAGCCGGCCTGGGTTCAAAGCTTCACCCCTTCTATTTATTTGATATTAGGTCATTC[C/T]
CTAATATTTGTGTTTTTAAAATTGGCATATACTAGCAAATATATGTTTTTCAACAGGAACTTTGTAGGATTGGGTTCTCGTGAGGTTTTTTTTGGCACTT

Reverse complement sequence

AAGTGCCAAAAAAAACCTCACGAGAACCCAATCCTACAAAGTTCCTGTTGAAAAACATATATTTGCTAGTATATGCCAATTTTAAAAACACAAATATTAG[G/A]
GAATGACCTAATATCAAATAAATAGAAGGGGTGAAGCTTTGAACCCAGGCCGGCTAGCCCACTAGCTTGTGGAGCTAGCTGGAAGACCCCTAAGAGTTTC

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 97.30% 1.70% 0.97% 0.00% NA
All Indica  2759 95.50% 2.90% 1.59% 0.00% NA
All Japonica  1512 99.90% 0.00% 0.07% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 83.50% 10.60% 5.88% 0.00% NA
Indica II  465 98.70% 0.60% 0.65% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 97.30% 1.90% 0.76% 0.00% NA
Temperate Japonica  767 99.90% 0.00% 0.13% 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 98.90% 0.00% 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
vg1014419290 C -> T LOC_Os10g27320.1 upstream_gene_variant ; 2025.0bp to feature; MODIFIER silent_mutation Average:41.166; most accessible tissue: Callus, score: 61.557 N N N N
vg1014419290 C -> T LOC_Os10g27330.1 upstream_gene_variant ; 4932.0bp to feature; MODIFIER silent_mutation Average:41.166; most accessible tissue: Callus, score: 61.557 N N N N
vg1014419290 C -> T LOC_Os10g27310-LOC_Os10g27320 intergenic_region ; MODIFIER silent_mutation Average:41.166; most accessible tissue: Callus, score: 61.557 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1014419290 NA 1.01E-07 mr1038 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
vg1014419290 NA 3.58E-08 mr1389 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
vg1014419290 1.83E-06 1.83E-06 mr1703 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
vg1014419290 NA 1.28E-08 mr1038_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
vg1014419290 NA 2.67E-07 mr1389_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