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Detailed information for vg0419773387:

Variant ID: vg0419773387 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 19773387
Reference Allele: TAlternative Allele: G
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.69, G: 0.30, others allele: 0.00, population size: 200. )

Flanking Sequence (100 bp) in Reference Genome:


GGGCGAATGTCACGTTGCGCAGATCCGGACCTCCACGACCAGATCTTGCGATGAGGCTTGCGAGCGGCAGGAAAGACAAAGGAGAGCCAGAGCTCGACGG[T/G]
GCGCATGTGGCAATGGTACAACGGTCGGTGCTGAAGGCGGTGTAAGGGACAGCCAGAGCTAGCATCCCAACGTCTAGATCCGGCATGCCCCTGACCGGAT

Reverse complement sequence

ATCCGGTCAGGGGCATGCCGGATCTAGACGTTGGGATGCTAGCTCTGGCTGTCCCTTACACCGCCTTCAGCACCGACCGTTGTACCATTGCCACATGCGC[A/C]
CCGTCGAGCTCTGGCTCTCCTTTGTCTTTCCTGCCGCTCGCAAGCCTCATCGCAAGATCTGGTCGTGGAGGTCCGGATCTGCGCAACGTGACATTCGCCC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 60.30% 39.30% 0.17% 0.21% NA
All Indica  2759 94.70% 4.90% 0.11% 0.25% NA
All Japonica  1512 0.30% 99.50% 0.13% 0.07% NA
Aus  269 67.30% 32.30% 0.37% 0.00% NA
Indica I  595 91.60% 8.10% 0.17% 0.17% NA
Indica II  465 93.50% 5.80% 0.00% 0.65% NA
Indica III  913 97.70% 2.10% 0.11% 0.11% NA
Indica Intermediate  786 94.30% 5.30% 0.13% 0.25% NA
Temperate Japonica  767 0.40% 99.50% 0.13% 0.00% NA
Tropical Japonica  504 0.40% 99.40% 0.00% 0.20% NA
Japonica Intermediate  241 0.00% 99.60% 0.41% 0.00% NA
VI/Aromatic  96 33.30% 66.70% 0.00% 0.00% NA
Intermediate  90 21.10% 74.40% 2.22% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0419773387 T -> DEL LOC_Os04g32780.1 N frameshift_variant Average:59.454; most accessible tissue: Zhenshan97 young leaf, score: 83.831 N N N N
vg0419773387 T -> G LOC_Os04g32780.1 synonymous_variant ; p.Gly55Gly; LOW synonymous_codon Average:59.454; most accessible tissue: Zhenshan97 young leaf, score: 83.831 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0419773387 NA 1.93E-79 mr1718 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
vg0419773387 NA 7.33E-16 mr1040_2 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
vg0419773387 NA 2.37E-07 mr1321_2 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
vg0419773387 NA 5.87E-20 mr1362_2 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
vg0419773387 NA 2.52E-07 mr1568_2 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
vg0419773387 NA 2.60E-21 mr1581_2 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
vg0419773387 NA 1.54E-22 mr1609_2 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
vg0419773387 NA 1.10E-16 mr1712_2 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
vg0419773387 NA 1.17E-12 mr1713_2 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
vg0419773387 NA 1.02E-108 mr1718_2 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
vg0419773387 NA 1.83E-49 mr1721_2 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
vg0419773387 NA 6.28E-17 mr1836_2 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
vg0419773387 NA 2.05E-06 mr1915_2 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