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Detailed information for vg0619892255:

Variant ID: vg0619892255 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 19892255
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 100. )

Flanking Sequence (100 bp) in Reference Genome:


ATAGAAAATTCGGCAAGTGGTCGCCGAATTGGGAAGGACCGTTCCAGATTCATAAAGTAGTGTCTAAAGGGGCTTACATGCTGCAAGGACTCGATGGTGA[G/A]
GTTTATGGAAGAGCATTGAATGGCAAATACTTGAAGAAATATTATCCAAGTGTTTGGGTTAATGCATGATTGGCTGATGTTGCCAATACATGATAGCCGA

Reverse complement sequence

TCGGCTATCATGTATTGGCAACATCAGCCAATCATGCATTAACCCAAACACTTGGATAATATTTCTTCAAGTATTTGCCATTCAATGCTCTTCCATAAAC[C/T]
TCACCATCGAGTCCTTGCAGCATGTAAGCCCCTTTAGACACTACTTTATGAATCTGGAACGGTCCTTCCCAATTCGGCGACCACTTGCCGAATTTTCTAT

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 34.60% 33.80% 1.25% 30.28% NA
All Indica  2759 58.10% 3.90% 1.59% 36.43% NA
All Japonica  1512 0.30% 95.40% 0.33% 3.90% NA
Aus  269 1.10% 0.40% 0.00% 98.51% NA
Indica I  595 47.40% 2.90% 1.85% 47.90% NA
Indica II  465 68.80% 4.50% 1.29% 25.38% NA
Indica III  913 63.60% 1.60% 0.99% 33.73% NA
Indica Intermediate  786 53.40% 6.90% 2.29% 37.40% NA
Temperate Japonica  767 0.40% 97.10% 0.00% 2.48% NA
Tropical Japonica  504 0.20% 92.30% 0.79% 6.75% NA
Japonica Intermediate  241 0.40% 96.70% 0.41% 2.49% NA
VI/Aromatic  96 7.30% 3.10% 9.38% 80.21% NA
Intermediate  90 21.10% 50.00% 1.11% 27.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0619892255 G -> A LOC_Os06g34140.1 synonymous_variant ; p.Glu1648Glu; LOW synonymous_codon Average:12.486; most accessible tissue: Callus, score: 31.68 N N N N
vg0619892255 G -> DEL LOC_Os06g34140.1 N frameshift_variant Average:12.486; most accessible tissue: Callus, score: 31.68 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0619892255 4.20E-06 1.01E-09 mr1033 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
vg0619892255 NA 1.22E-06 mr1064 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
vg0619892255 NA 1.09E-07 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
vg0619892255 7.43E-06 NA mr1112 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
vg0619892255 NA 8.34E-08 mr1176 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
vg0619892255 NA 1.53E-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
vg0619892255 NA 1.01E-17 mr1253 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
vg0619892255 NA 4.58E-06 mr1534 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
vg0619892255 NA 3.85E-06 mr1560 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
vg0619892255 NA 3.73E-49 mr1599 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
vg0619892255 NA 1.34E-09 mr1663 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
vg0619892255 NA 1.24E-12 mr1949 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
vg0619892255 NA 4.47E-06 mr1970 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
vg0619892255 8.20E-09 4.20E-09 mr1973 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
vg0619892255 NA 3.17E-22 mr1949_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