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Detailed information for vg0410451060:

Variant ID: vg0410451060 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 10451060
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTGGAGGTTGAGGACTCCTAGACGGCTAGGTGTCACTCCCGAGCCACCGATCTACGTGTGGTTGGCCGAGAGAAGTTTGTGAAGGCCGGATCTCGCCTCC[G/A]
CAAGGAAAGAGATACCCCTTAGTGGAAGGAGGAGTGCTTAGTGCAACCTCTTGAGGAAAGGGTTAGCAAAGACCCGGCTCTTAGTGAGCTCCTCAACGGA

Reverse complement sequence

TCCGTTGAGGAGCTCACTAAGAGCCGGGTCTTTGCTAACCCTTTCCTCAAGAGGTTGCACTAAGCACTCCTCCTTCCACTAAGGGGTATCTCTTTCCTTG[C/T]
GGAGGCGAGATCCGGCCTTCACAAACTTCTCTCGGCCAACCACACGTAGATCGGTGGCTCGGGAGTGACACCTAGCCGTCTAGGAGTCCTCAACCTCCAA

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 85.50% 14.50% 0.04% 0.00% NA
All Indica  2759 99.60% 0.40% 0.00% 0.00% NA
All Japonica  1512 62.20% 37.70% 0.07% 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 99.10% 0.90% 0.00% 0.00% NA
Indica III  913 99.80% 0.20% 0.00% 0.00% NA
Indica Intermediate  786 99.40% 0.60% 0.00% 0.00% NA
Temperate Japonica  767 96.30% 3.70% 0.00% 0.00% NA
Tropical Japonica  504 6.20% 93.80% 0.00% 0.00% NA
Japonica Intermediate  241 71.00% 28.60% 0.41% 0.00% NA
VI/Aromatic  96 15.60% 84.40% 0.00% 0.00% NA
Intermediate  90 74.40% 24.40% 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
vg0410451060 G -> A LOC_Os04g18800.1 upstream_gene_variant ; 2938.0bp to feature; MODIFIER silent_mutation Average:38.514; most accessible tissue: Zhenshan97 flower, score: 58.632 N N N N
vg0410451060 G -> A LOC_Os04g18790.1 downstream_gene_variant ; 1205.0bp to feature; MODIFIER silent_mutation Average:38.514; most accessible tissue: Zhenshan97 flower, score: 58.632 N N N N
vg0410451060 G -> A LOC_Os04g18780-LOC_Os04g18790 intergenic_region ; MODIFIER silent_mutation Average:38.514; most accessible tissue: Zhenshan97 flower, score: 58.632 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0410451060 NA 1.29E-06 mr1319 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
vg0410451060 NA 9.04E-13 mr1454 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
vg0410451060 NA 8.13E-06 mr1508 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
vg0410451060 NA 2.22E-07 mr1668 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
vg0410451060 NA 3.30E-08 mr1786 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