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Detailed information for vg0728428950:

Variant ID: vg0728428950 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 28428950
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.73, A: 0.26, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:


GACATACACTATTGCTTGAATTAATATGGTTCTTGGATATATTTCATTTTTCTTTTCAGGGACAGTCTTCAAAGTCGAAGGAATCTGAGTCGTACAAAAA[A/G]
GGTAAGACTATGCATGTACTATTAGTTATATGCACAGACTCACTGAGTAGTGACTGCTTTGGTCGCTATGTATGCCTAGTTTAAGTAGAAAATCATTGAG

Reverse complement sequence

CTCAATGATTTTCTACTTAAACTAGGCATACATAGCGACCAAAGCAGTCACTACTCAGTGAGTCTGTGCATATAACTAATAGTACATGCATAGTCTTACC[T/C]
TTTTTGTACGACTCAGATTCCTTCGACTTTGAAGACTGTCCCTGAAAAGAAAAATGAAATATATCCAAGAACCATATTAATTCAAGCAATAGTGTATGTC

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 57.60% 42.20% 0.11% 0.02% NA
All Indica  2759 93.20% 6.70% 0.11% 0.00% NA
All Japonica  1512 1.70% 98.30% 0.00% 0.00% NA
Aus  269 9.30% 90.30% 0.00% 0.37% NA
Indica I  595 99.20% 0.70% 0.17% 0.00% NA
Indica II  465 96.10% 3.90% 0.00% 0.00% NA
Indica III  913 92.40% 7.60% 0.00% 0.00% NA
Indica Intermediate  786 87.90% 11.80% 0.25% 0.00% NA
Temperate Japonica  767 1.00% 99.00% 0.00% 0.00% NA
Tropical Japonica  504 2.60% 97.40% 0.00% 0.00% NA
Japonica Intermediate  241 1.70% 98.30% 0.00% 0.00% NA
VI/Aromatic  96 61.50% 38.50% 0.00% 0.00% NA
Intermediate  90 47.80% 50.00% 2.22% 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
vg0728428950 A -> DEL LOC_Os07g47530.2 N frameshift_variant Average:50.569; most accessible tissue: Callus, score: 73.156 N N N N
vg0728428950 A -> DEL LOC_Os07g47530.1 N frameshift_variant Average:50.569; most accessible tissue: Callus, score: 73.156 N N N N
vg0728428950 A -> G LOC_Os07g47530.1 splice_region_variant&synonymous_variant ; p.Lys429Lys; LOW synonymous_codon Average:50.569; most accessible tissue: Callus, score: 73.156 N N N N
vg0728428950 A -> G LOC_Os07g47530.2 splice_region_variant&synonymous_variant ; p.Lys429Lys; LOW synonymous_codon Average:50.569; most accessible tissue: Callus, score: 73.156 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0728428950 NA 1.24E-52 mr1063 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
vg0728428950 NA 4.96E-34 mr1404 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
vg0728428950 NA 7.62E-10 mr1524 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
vg0728428950 NA 1.57E-20 mr1580 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
vg0728428950 NA 8.77E-31 mr1745 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
vg0728428950 NA 3.78E-18 mr1825 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
vg0728428950 NA 3.06E-08 mr1827 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
vg0728428950 NA 1.45E-15 mr1870 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
vg0728428950 NA 3.71E-21 mr1943 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
vg0728428950 NA 1.58E-56 mr1063_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
vg0728428950 NA 7.48E-64 mr1078_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
vg0728428950 NA 1.44E-44 mr1094_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
vg0728428950 NA 1.16E-58 mr1096_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
vg0728428950 NA 6.40E-22 mr1164_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
vg0728428950 NA 6.93E-09 mr1172_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
vg0728428950 NA 2.27E-20 mr1183_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
vg0728428950 NA 1.27E-16 mr1260_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
vg0728428950 2.36E-06 5.31E-21 mr1531_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
vg0728428950 NA 1.00E-33 mr1580_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
vg0728428950 NA 3.63E-15 mr1807_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
vg0728428950 NA 1.47E-34 mr1825_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
vg0728428950 NA 3.24E-18 mr1870_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