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Detailed information for vg0619888183:

Variant ID: vg0619888183 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 19888183
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:


ATCAAAGATTGGGTCCAGTGAATCAAGATCATGGCCAAGAGGACAATGAAATCAGGAAAAATCAGTGGTGTCCTTCTGGTATTTTCACGAAGAATCAGAA[G/A]
AGAAGGGTTCAAAGATTGAGGAACAGGGAGCGATTTCAGGAGGTTGAACAGGAAATTAACCATCGGCTGAAGAGAACAAAGCCGAGGCAGGAGTGGCGCG

Reverse complement sequence

CGCGCCACTCCTGCCTCGGCTTTGTTCTCTTCAGCCGATGGTTAATTTCCTGTTCAACCTCCTGAAATCGCTCCCTGTTCCTCAATCTTTGAACCCTTCT[C/T]
TTCTGATTCTTCGTGAAAATACCAGAAGGACACCACTGATTTTTCCTGATTTCATTGTCCTCTTGGCCATGATCTTGATTCACTGGACCCAATCTTTGAT

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 36.20% 9.20% 12.48% 42.04% NA
All Indica  2759 7.80% 4.50% 18.63% 69.08% NA
All Japonica  1512 95.90% 1.30% 0.33% 2.45% NA
Aus  269 0.40% 98.90% 0.37% 0.37% NA
Indica I  595 3.40% 0.20% 17.82% 78.66% NA
Indica II  465 8.00% 3.20% 18.92% 69.89% NA
Indica III  913 9.60% 4.10% 19.39% 66.92% NA
Indica Intermediate  786 9.00% 8.90% 18.19% 63.87% NA
Temperate Japonica  767 97.10% 0.00% 0.26% 2.61% NA
Tropical Japonica  504 93.50% 4.00% 0.20% 2.38% NA
Japonica Intermediate  241 97.10% 0.00% 0.83% 2.07% NA
VI/Aromatic  96 1.00% 24.00% 59.38% 15.62% NA
Intermediate  90 50.00% 4.40% 14.44% 31.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0619888183 G -> A LOC_Os06g34140.1 synonymous_variant ; p.Lys538Lys; LOW synonymous_codon Average:9.516; most accessible tissue: Callus, score: 29.502 N N N N
vg0619888183 G -> DEL LOC_Os06g34140.1 N frameshift_variant Average:9.516; most accessible tissue: Callus, score: 29.502 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0619888183 NA 8.61E-06 mr1076 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
vg0619888183 NA 2.58E-06 mr1082 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
vg0619888183 NA 1.53E-06 mr1086 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
vg0619888183 NA 1.31E-20 mr1102 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
vg0619888183 NA 7.14E-06 mr1103 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
vg0619888183 NA 9.10E-07 mr1145 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
vg0619888183 NA 9.41E-06 mr1204 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
vg0619888183 NA 2.91E-07 mr1226 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
vg0619888183 NA 5.16E-08 mr1411 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
vg0619888183 2.34E-06 1.07E-23 mr1805 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
vg0619888183 2.61E-06 1.95E-08 mr1805 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
vg0619888183 NA 1.09E-06 mr1878 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