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Detailed information for vg0714475265:

Variant ID: vg0714475265 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 14475265
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATAGAGGAGGATGCCGGCCTGAGGTTAGGGAAGGGTCCGACATGTGGGGCCCACATGTCGGTCTCCAGAGTGGAGGGGCGGCTGGCGGGCTGGCTGGGCC[G/A]
GCTTGGCCACGGGTGAGAGAGGGAGAGTTGGGCCAAAAACGGCCCAACAACTTAAGGAGGGGTTTTTGGAACTTTTCAACTAAAATAATTTGTGAAATGT

Reverse complement sequence

ACATTTCACAAATTATTTTAGTTGAAAAGTTCCAAAAACCCCTCCTTAAGTTGTTGGGCCGTTTTTGGCCCAACTCTCCCTCTCTCACCCGTGGCCAAGC[C/T]
GGCCCAGCCAGCCCGCCAGCCGCCCCTCCACTCTGGAGACCGACATGTGGGCCCCACATGTCGGACCCTTCCCTAACCTCAGGCCGGCATCCTCCTCTAT

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 76.30% 6.50% 11.02% 6.20% NA
All Indica  2759 68.50% 11.00% 16.27% 4.24% NA
All Japonica  1512 84.50% 0.20% 3.77% 11.51% NA
Aus  269 98.50% 0.00% 1.49% 0.00% NA
Indica I  595 94.30% 2.40% 3.36% 0.00% NA
Indica II  465 56.10% 11.00% 24.30% 8.60% NA
Indica III  913 57.50% 16.40% 21.03% 5.04% NA
Indica Intermediate  786 69.10% 11.20% 15.78% 3.94% NA
Temperate Japonica  767 82.10% 0.30% 3.52% 14.08% NA
Tropical Japonica  504 95.20% 0.00% 1.79% 2.98% NA
Japonica Intermediate  241 69.70% 0.40% 8.71% 21.16% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 83.30% 2.20% 12.22% 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
vg0714475265 G -> DEL LOC_Os07g25340.1 N frameshift_variant Average:19.91; most accessible tissue: Callus, score: 40.044 N N N N
vg0714475265 G -> A LOC_Os07g25340.1 synonymous_variant ; p.Pro20Pro; LOW synonymous_codon Average:19.91; most accessible tissue: Callus, score: 40.044 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0714475265 1.11E-06 1.11E-06 mr1313 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
vg0714475265 3.51E-06 3.51E-06 mr1473 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
vg0714475265 2.08E-06 2.08E-06 mr1664 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
vg0714475265 9.45E-08 9.45E-08 mr1848 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
vg0714475265 4.86E-06 4.86E-06 mr1279_2 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
vg0714475265 5.54E-06 5.54E-06 mr1313_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
vg0714475265 2.53E-07 2.53E-07 mr1473_2 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
vg0714475265 3.06E-07 3.06E-07 mr1630_2 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
vg0714475265 1.82E-09 1.82E-09 mr1848_2 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