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Detailed information for vg0517993776:

Variant ID: vg0517993776 (JBrowse)Variation Type: INDEL
Chromosome: chr05Position: 17993776
Reference Allele: GAlternative Allele: A,GTATT
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, A: 0.03, others allele: 0.00, population size: 62. )

Flanking Sequence (100 bp) in Reference Genome:


CATGCGGGTTTTTTTAAAAAAGGTTTTCTTATACGACTCCTTATATATTTCTAAAAACAAATGAATTTAAAAATTAACTCAAATACGGACGATGTACCAA[G/A,GTATT]
GTATTGGTATAAACATCTTGATTTTTTATAATAGTAGAGAAGAGGTAAATGACTCGATCATGATTCCATTTATTTACAATAAATAAATAATGGAGCAAAT

Reverse complement sequence

ATTTGCTCCATTATTTATTTATTGTAAATAAATGGAATCATGATCGAGTCATTTACCTCTTCTCTACTATTATAAAAAATCAAGATGTTTATACCAATAC[C/T,AATAC]
TTGGTACATCGTCCGTATTTGAGTTAATTTTTAAATTCATTTGTTTTTAGAAATATATAAGGAGTCGTATAAGAAAACCTTTTTTAAAAAAACCCGCATG

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 83.00% 12.20% 2.45% 0.00% GTATT: 2.31%
All Indica  2759 95.00% 4.70% 0.33% 0.00% NA
All Japonica  1512 57.40% 28.40% 7.01% 0.00% GTATT: 7.14%
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 76.10% 21.90% 1.94% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 96.60% 3.40% 0.00% 0.00% NA
Temperate Japonica  767 79.00% 7.40% 7.69% 0.00% GTATT: 5.87%
Tropical Japonica  504 38.10% 54.00% 3.57% 0.00% GTATT: 4.37%
Japonica Intermediate  241 29.00% 41.90% 12.03% 0.00% GTATT: 17.01%
VI/Aromatic  96 95.80% 4.20% 0.00% 0.00% NA
Intermediate  90 81.10% 16.70% 1.11% 0.00% GTATT: 1.11%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0517993776 G -> GTATT LOC_Os05g30980.1 upstream_gene_variant ; 1426.0bp to feature; MODIFIER silent_mutation Average:43.407; most accessible tissue: Minghui63 panicle, score: 59.629 N N N N
vg0517993776 G -> GTATT LOC_Os05g30980.2 upstream_gene_variant ; 1880.0bp to feature; MODIFIER silent_mutation Average:43.407; most accessible tissue: Minghui63 panicle, score: 59.629 N N N N
vg0517993776 G -> GTATT LOC_Os05g30970.1 downstream_gene_variant ; 3866.0bp to feature; MODIFIER silent_mutation Average:43.407; most accessible tissue: Minghui63 panicle, score: 59.629 N N N N
vg0517993776 G -> GTATT LOC_Os05g30970-LOC_Os05g30980 intergenic_region ; MODIFIER silent_mutation Average:43.407; most accessible tissue: Minghui63 panicle, score: 59.629 N N N N
vg0517993776 G -> A LOC_Os05g30980.1 upstream_gene_variant ; 1427.0bp to feature; MODIFIER silent_mutation Average:43.407; most accessible tissue: Minghui63 panicle, score: 59.629 N N N N
vg0517993776 G -> A LOC_Os05g30980.2 upstream_gene_variant ; 1881.0bp to feature; MODIFIER silent_mutation Average:43.407; most accessible tissue: Minghui63 panicle, score: 59.629 N N N N
vg0517993776 G -> A LOC_Os05g30970.1 downstream_gene_variant ; 3865.0bp to feature; MODIFIER silent_mutation Average:43.407; most accessible tissue: Minghui63 panicle, score: 59.629 N N N N
vg0517993776 G -> A LOC_Os05g30970-LOC_Os05g30980 intergenic_region ; MODIFIER silent_mutation Average:43.407; most accessible tissue: Minghui63 panicle, score: 59.629 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0517993776 NA 6.11E-06 mr1002 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
vg0517993776 NA 4.01E-08 mr1039 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
vg0517993776 NA 5.08E-07 mr1044 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
vg0517993776 NA 1.04E-06 mr1077 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
vg0517993776 NA 2.66E-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
vg0517993776 NA 8.32E-07 mr1399 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
vg0517993776 NA 3.54E-06 mr1408 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
vg0517993776 NA 5.95E-06 mr1482 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
vg0517993776 4.36E-06 4.35E-06 mr1562 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
vg0517993776 NA 9.30E-06 mr1602 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
vg0517993776 NA 1.82E-06 mr1632 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
vg0517993776 NA 4.33E-07 mr1726 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
vg0517993776 2.88E-06 2.88E-06 mr1952 Jap_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
vg0517993776 NA 8.09E-06 mr1002_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
vg0517993776 NA 1.20E-07 mr1039_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
vg0517993776 NA 1.01E-06 mr1363_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
vg0517993776 NA 5.94E-06 mr1399_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
vg0517993776 NA 5.49E-06 mr1544_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
vg0517993776 NA 1.38E-07 mr1794_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