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Detailed information for vg0428353570:

Variant ID: vg0428353570 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 28353570
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTGTGAAAACTAAAATGGCCTATATTTATGTGAGGATTTGATCCTTCTATGTGGCATGAGGTAACCCAGACTCGGTTTGGAAAGGCTTTGTCGTGAACCT[C/T]
TGACACCGGCCAGTGTCTGGAGTAAGTTCGTGTCTTGTGGGTAAAGTGTACCCCTCTGCAGAGGTTAACTAACTGTTCGAACAGCCGTGCCCACGGTCAT

Reverse complement sequence

ATGACCGTGGGCACGGCTGTTCGAACAGTTAGTTAACCTCTGCAGAGGGGTACACTTTACCCACAAGACACGAACTTACTCCAGACACTGGCCGGTGTCA[G/A]
AGGTTCACGACAAAGCCTTTCCAAACCGAGTCTGGGTTACCTCATGCCACATAGAAGGATCAAATCCTCACATAAATATAGGCCATTTTAGTTTTCACAA

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 56.60% 43.30% 0.02% 0.02% NA
All Indica  2759 26.70% 73.20% 0.04% 0.04% NA
All Japonica  1512 99.80% 0.20% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 28.10% 71.80% 0.00% 0.17% NA
Indica II  465 9.70% 90.30% 0.00% 0.00% NA
Indica III  913 28.30% 71.70% 0.00% 0.00% NA
Indica Intermediate  786 34.10% 65.80% 0.13% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 71.10% 28.90% 0.00% 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
vg0428353570 C -> DEL N N silent_mutation Average:39.881; most accessible tissue: Zhenshan97 flag leaf, score: 68.25 N N N N
vg0428353570 C -> T LOC_Os04g47790.1 upstream_gene_variant ; 1939.0bp to feature; MODIFIER silent_mutation Average:39.881; most accessible tissue: Zhenshan97 flag leaf, score: 68.25 N N N N
vg0428353570 C -> T LOC_Os04g47780-LOC_Os04g47790 intergenic_region ; MODIFIER silent_mutation Average:39.881; most accessible tissue: Zhenshan97 flag leaf, score: 68.25 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0428353570 NA 2.37E-06 mr1011 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
vg0428353570 NA 9.98E-11 mr1125 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
vg0428353570 NA 1.18E-29 mr1237 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
vg0428353570 NA 7.34E-06 mr1398 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
vg0428353570 NA 1.76E-17 mr1552 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
vg0428353570 NA 1.51E-06 mr1094_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
vg0428353570 NA 1.68E-07 mr1125_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