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Detailed information for vg0728250817:

Variant ID: vg0728250817 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 28250817
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.91, A: 0.09, others allele: 0.00, population size: 272. )

Flanking Sequence (100 bp) in Reference Genome:


TACTGCCACTGCCATAACCTTCACTGTGATCCTGCTCGAATTCCCCTCTAGTAGTTTCCTTCCTCCCCAAGTCTGGGAAGTTCCAGTTAAGTGAATCGGC[A/G]
GCATGTTGGGCATCAGGAACACTGGTTGTTCGTCGATGTGCTTTTGCCTTTGGGGTGGATGGGCAAGTCCTCGAACTCTTTGCAGAAGGTGCATTAGGAT

Reverse complement sequence

ATCCTAATGCACCTTCTGCAAAGAGTTCGAGGACTTGCCCATCCACCCCAAAGGCAAAAGCACATCGACGAACAACCAGTGTTCCTGATGCCCAACATGC[T/C]
GCCGATTCACTTAACTGGAACTTCCCAGACTTGGGGAGGAAGGAAACTACTAGAGGGGAATTCGAGCAGGATCACAGTGAAGGTTATGGCAGTGGCAGTA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 53.00% 46.50% 0.28% 0.28% NA
All Indica  2759 43.60% 55.60% 0.36% 0.43% NA
All Japonica  1512 68.00% 31.90% 0.07% 0.00% NA
Aus  269 50.60% 49.40% 0.00% 0.00% NA
Indica I  595 58.70% 41.00% 0.34% 0.00% NA
Indica II  465 24.50% 74.40% 0.43% 0.65% NA
Indica III  913 47.60% 51.50% 0.33% 0.55% NA
Indica Intermediate  786 38.90% 60.20% 0.38% 0.51% NA
Temperate Japonica  767 96.10% 3.90% 0.00% 0.00% NA
Tropical Japonica  504 22.60% 77.20% 0.20% 0.00% NA
Japonica Intermediate  241 73.40% 26.60% 0.00% 0.00% NA
VI/Aromatic  96 78.10% 20.80% 1.04% 0.00% NA
Intermediate  90 66.70% 31.10% 1.11% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0728250817 A -> DEL LOC_Os07g47270.1 N frameshift_variant Average:60.74; most accessible tissue: Callus, score: 81.802 N N N N
vg0728250817 A -> G LOC_Os07g47270.1 synonymous_variant ; p.Ala394Ala; LOW synonymous_codon Average:60.74; most accessible tissue: Callus, score: 81.802 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0728250817 NA 7.19E-06 mr1075 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
vg0728250817 NA 2.53E-06 mr1124 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
vg0728250817 NA 2.42E-06 mr1277 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
vg0728250817 NA 1.37E-07 mr1551 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
vg0728250817 NA 6.30E-07 mr1584 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
vg0728250817 NA 1.06E-13 mr1879 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
vg0728250817 NA 1.01E-08 mr1304_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
vg0728250817 NA 1.40E-07 mr1308_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
vg0728250817 NA 2.82E-09 mr1361_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
vg0728250817 NA 1.50E-12 mr1368_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
vg0728250817 NA 3.67E-15 mr1540_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
vg0728250817 NA 2.96E-10 mr1584_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
vg0728250817 NA 1.57E-06 mr1629_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
vg0728250817 NA 2.79E-06 mr1730_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
vg0728250817 NA 3.07E-14 mr1732_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
vg0728250817 NA 2.02E-06 mr1866_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
vg0728250817 NA 2.10E-10 mr1879_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
vg0728250817 NA 3.97E-10 mr1942_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