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Detailed information for vg0800072058:

Variant ID: vg0800072058 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 72058
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.86, A: 0.15, others allele: 0.00, population size: 277. )

Flanking Sequence (100 bp) in Reference Genome:


ACTCGGCCTTGAGCTCTGCAGCCTTGTCCAAGTAAGGCTTCTTGTCCTCGTCAGACATGGATTTCCACCTCTCCCCTCCTTCCTTGGCGACAGCGGAGAC[G/A]
CTCTTGTTGTCAGGGTGCTCCGCCTTGTACTCCTTCCTGAAGTCACTCCTGCATATTAAGCATATCATACATCTTCTTCTTCTTCTTCCATGGGAATGGA

Reverse complement sequence

TCCATTCCCATGGAAGAAGAAGAAGAAGATGTATGATATGCTTAATATGCAGGAGTGACTTCAGGAAGGAGTACAAGGCGGAGCACCCTGACAACAAGAG[C/T]
GTCTCCGCTGTCGCCAAGGAAGGAGGGGAGAGGTGGAAATCCATGTCTGACGAGGACAAGAAGCCTTACTTGGACAAGGCTGCAGAGCTCAAGGCCGAGT

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 61.70% 38.00% 0.04% 0.28% NA
All Indica  2759 46.20% 53.30% 0.07% 0.47% NA
All Japonica  1512 87.80% 12.20% 0.00% 0.00% NA
Aus  269 61.30% 38.70% 0.00% 0.00% NA
Indica I  595 66.10% 33.40% 0.00% 0.50% NA
Indica II  465 25.20% 74.60% 0.00% 0.22% NA
Indica III  913 45.90% 53.60% 0.11% 0.44% NA
Indica Intermediate  786 43.90% 55.30% 0.13% 0.64% NA
Temperate Japonica  767 97.30% 2.70% 0.00% 0.00% NA
Tropical Japonica  504 72.40% 27.60% 0.00% 0.00% NA
Japonica Intermediate  241 90.00% 10.00% 0.00% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 61.10% 38.90% 0.00% 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
vg0800072058 G -> A LOC_Os08g01100.1 synonymous_variant ; p.Ser119Ser; LOW synonymous_codon Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0800072058 G -> DEL LOC_Os08g01100.1 N frameshift_variant Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0800072058 NA 5.19E-06 mr1057 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
vg0800072058 8.87E-11 6.62E-16 mr1277 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
vg0800072058 7.88E-10 1.56E-08 mr1277 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
vg0800072058 3.17E-20 1.67E-35 mr1746 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
vg0800072058 3.54E-15 1.60E-20 mr1746 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
vg0800072058 NA 1.85E-11 mr1746 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
vg0800072058 NA 4.55E-13 mr1769 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
vg0800072058 NA 1.63E-06 mr1805 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
vg0800072058 NA 7.48E-13 mr1055_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
vg0800072058 5.64E-08 NA mr1277_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
vg0800072058 1.44E-06 NA mr1277_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
vg0800072058 NA 2.79E-07 mr1632_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
vg0800072058 NA 2.32E-08 mr1676_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
vg0800072058 5.48E-23 1.49E-43 mr1746_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
vg0800072058 8.13E-19 2.72E-27 mr1746_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
vg0800072058 NA 1.16E-09 mr1746_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
vg0800072058 NA 1.67E-13 mr1769_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