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Detailed information for vg0415203314:

Variant ID: vg0415203314 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 15203314
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CGAAGTCACCATTGATTCTATGGCGAACATGGATGTCAGCGGTGGCATGACCATTGAGGGTCTCTGTTCAGTGGAGATGAAAGAAGCAAGTTGGCCTTGA[T/C]
GATGTAGCAGTGGACTCAGACATGTCGAGTTGAACACTGCCGATGCTATATATGCATCCTAGAGGCTTGTTGCAAGCGACATTGTGATGTCCGTGGGCTA

Reverse complement sequence

TAGCCCACGGACATCACAATGTCGCTTGCAACAAGCCTCTAGGATGCATATATAGCATCGGCAGTGTTCAACTCGACATGTCTGAGTCCACTGCTACATC[A/G]
TCAAGGCCAACTTGCTTCTTTCATCTCCACTGAACAGAGACCCTCAATGGTCATGCCACCGCTGACATCCATGTTCGCCATAGAATCAATGGTGACTTCG

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 76.40% 0.60% 3.66% 19.30% NA
All Indica  2759 77.30% 0.90% 3.33% 18.41% NA
All Japonica  1512 86.30% 0.10% 1.19% 12.37% NA
Aus  269 6.30% 0.00% 20.45% 73.23% NA
Indica I  595 98.30% 0.00% 1.68% 0.00% NA
Indica II  465 71.00% 3.40% 5.59% 20.00% NA
Indica III  913 64.60% 0.30% 3.40% 31.65% NA
Indica Intermediate  786 80.00% 0.80% 3.18% 16.03% NA
Temperate Japonica  767 77.40% 0.10% 1.96% 20.47% NA
Tropical Japonica  504 95.20% 0.20% 0.40% 4.17% NA
Japonica Intermediate  241 95.90% 0.00% 0.41% 3.73% NA
VI/Aromatic  96 86.50% 0.00% 4.17% 9.38% NA
Intermediate  90 80.00% 3.30% 4.44% 12.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0415203314 T -> C LOC_Os04g26110.1 intron_variant ; MODIFIER silent_mutation Average:50.675; most accessible tissue: Minghui63 flag leaf, score: 68.675 N N N N
vg0415203314 T -> DEL N N silent_mutation Average:50.675; most accessible tissue: Minghui63 flag leaf, score: 68.675 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0415203314 NA 3.51E-06 mr1080 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
vg0415203314 NA 7.01E-07 mr1100 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
vg0415203314 NA 4.64E-06 mr1140 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
vg0415203314 NA 3.17E-06 mr1203 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
vg0415203314 NA 4.39E-06 mr1395 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
vg0415203314 1.91E-06 2.07E-09 mr1613 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
vg0415203314 NA 3.67E-07 mr1619 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
vg0415203314 4.68E-08 4.68E-08 mr1795 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
vg0415203314 NA 1.45E-06 mr1913 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
vg0415203314 NA 7.65E-07 mr1962 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
vg0415203314 NA 2.79E-07 mr1100_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