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Detailed information for vg0142615783:

Variant ID: vg0142615783 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 42615783
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.87, A: 0.13, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:


GTTTGGTTTATCAGGTGGCCTTTGCCAGAGAAGAAGTTCAGGAGCTACAGAAGAACCCTGAGAGATTTCTTCAGGAATCACTTAATCTAGTTGGATACAC[A/G]
GGTGCTCTTGCAAATCCACTAGTAGCCCCTGAGGAGAGTCTCACACGAATCAATGGCAGTATTATTCAAAAGTTCTATCACGTAATTCTCTTGCTTCTGT

Reverse complement sequence

ACAGAAGCAAGAGAATTACGTGATAGAACTTTTGAATAATACTGCCATTGATTCGTGTGAGACTCTCCTCAGGGGCTACTAGTGGATTTGCAAGAGCACC[T/C]
GTGTATCCAACTAGATTAAGTGATTCCTGAAGAAATCTCTCAGGGTTCTTCTGTAGCTCCTGAACTTCTTCTCTGGCAAAGGCCACCTGATAAACCAAAC

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 63.20% 36.40% 0.32% 0.11% NA
All Indica  2759 56.90% 42.50% 0.43% 0.14% NA
All Japonica  1512 88.10% 11.80% 0.07% 0.00% NA
Aus  269 6.30% 93.70% 0.00% 0.00% NA
Indica I  595 89.70% 9.90% 0.34% 0.00% NA
Indica II  465 26.00% 72.70% 0.86% 0.43% NA
Indica III  913 47.80% 52.00% 0.22% 0.00% NA
Indica Intermediate  786 60.90% 38.30% 0.51% 0.25% NA
Temperate Japonica  767 94.30% 5.70% 0.00% 0.00% NA
Tropical Japonica  504 76.00% 23.80% 0.20% 0.00% NA
Japonica Intermediate  241 93.80% 6.20% 0.00% 0.00% NA
VI/Aromatic  96 24.00% 76.00% 0.00% 0.00% NA
Intermediate  90 50.00% 46.70% 2.22% 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
vg0142615783 A -> G LOC_Os01g73550.1 synonymous_variant ; p.Thr209Thr; LOW synonymous_codon Average:70.027; most accessible tissue: Callus, score: 81.361 N N N N
vg0142615783 A -> G LOC_Os01g73550.2 synonymous_variant ; p.Thr209Thr; LOW synonymous_codon Average:70.027; most accessible tissue: Callus, score: 81.361 N N N N
vg0142615783 A -> DEL LOC_Os01g73550.1 N frameshift_variant Average:70.027; most accessible tissue: Callus, score: 81.361 N N N N
vg0142615783 A -> DEL LOC_Os01g73550.2 N frameshift_variant Average:70.027; most accessible tissue: Callus, score: 81.361 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0142615783 NA 3.58E-06 mr1170 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
vg0142615783 NA 7.61E-06 mr1188 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
vg0142615783 NA 1.99E-06 mr1291 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
vg0142615783 NA 1.48E-06 mr1629 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
vg0142615783 NA 1.91E-06 mr1919 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
vg0142615783 NA 8.68E-06 mr1919 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
vg0142615783 NA 7.38E-08 mr1974 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
vg0142615783 2.28E-07 1.21E-13 mr1974 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
vg0142615783 NA 1.46E-07 mr1984 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
vg0142615783 NA 2.74E-09 mr1188_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
vg0142615783 NA 2.54E-06 mr1850_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
vg0142615783 NA 2.65E-06 mr1931_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
vg0142615783 NA 8.66E-07 mr1942_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
vg0142615783 NA 2.51E-09 mr1974_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