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Detailed information for vg0128850364:

Variant ID: vg0128850364 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 28850364
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTTGGAAGTTTGAAGAAAAATTTTATAACTAAACACGGCCTTGATGTGATGGAAAAGTTAGAAGTTTGAAGAAAATTTTTGGAACTATGTGTTTAGTTCA[C/T]
GCTAAAATTTAAAGTTTTATTAAAATTGGAACAATGTGATAAAAAAGTTGAAAATTTTAAGAAAAAACGAGCATGGTGGCCCGCGCAGATTGCACGGCCA

Reverse complement sequence

TGGCCGTGCAATCTGCGCGGGCCACCATGCTCGTTTTTTCTTAAAATTTTCAACTTTTTTATCACATTGTTCCAATTTTAATAAAACTTTAAATTTTAGC[G/A]
TGAACTAAACACATAGTTCCAAAAATTTTCTTCAAACTTCTAACTTTTCCATCACATCAAGGCCGTGTTTAGTTATAAAATTTTTCTTCAAACTTCCAAC

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 95.90% 3.90% 0.17% 0.00% NA
All Indica  2759 99.30% 0.70% 0.00% 0.00% NA
All Japonica  1512 90.10% 9.50% 0.46% 0.00% NA
Aus  269 94.40% 5.60% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 98.30% 1.70% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 98.60% 1.40% 0.00% 0.00% NA
Temperate Japonica  767 99.10% 0.70% 0.26% 0.00% NA
Tropical Japonica  504 74.80% 24.20% 0.99% 0.00% NA
Japonica Intermediate  241 93.40% 6.60% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 88.90% 10.00% 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
vg0128850364 C -> T LOC_Os01g50190.1 upstream_gene_variant ; 3421.0bp to feature; MODIFIER silent_mutation Average:40.024; most accessible tissue: Minghui63 panicle, score: 76.913 N N N N
vg0128850364 C -> T LOC_Os01g50200.1 upstream_gene_variant ; 540.0bp to feature; MODIFIER silent_mutation Average:40.024; most accessible tissue: Minghui63 panicle, score: 76.913 N N N N
vg0128850364 C -> T LOC_Os01g50220.1 downstream_gene_variant ; 4385.0bp to feature; MODIFIER silent_mutation Average:40.024; most accessible tissue: Minghui63 panicle, score: 76.913 N N N N
vg0128850364 C -> T LOC_Os01g50200-LOC_Os01g50220 intergenic_region ; MODIFIER silent_mutation Average:40.024; most accessible tissue: Minghui63 panicle, score: 76.913 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0128850364 NA 5.54E-06 mr1188 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
vg0128850364 NA 4.46E-06 mr1217_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
vg0128850364 NA 1.95E-06 mr1633_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
vg0128850364 1.07E-06 9.07E-09 mr1696_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