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Detailed information for vg0317005591:

Variant ID: vg0317005591 (JBrowse)Variation Type: INDEL
Chromosome: chr03Position: 17005591
Reference Allele: TAlternative Allele: C,TGTGACCCACCTATGTGACCCCGGAGACTTGTTACCTGGCCTCTCC
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.63, C: 0.37, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:


AAGACTTGTTACCTGGTCTCTCCACCATGTGACCCGGGTTCCACCTTTTAAGTCGTCACATCAACCTATGTGACCCCGGAGACTTGTTACCTGGCCTCTC[T/C,TGTGACCCACCTATGTGACCCCGGAGACTTGTTACCTGGCCTCTCC]
ACCATGTGACCCATGGAAATTGTTCCGGGTTCCAAACCTTGGGCTCTGATACCCACTTGTTAGAGTGCGCAGCCCGGCCCACCAACCGTGGGCCACAACT

Reverse complement sequence

AGTTGTGGCCCACGGTTGGTGGGCCGGGCTGCGCACTCTAACAAGTGGGTATCAGAGCCCAAGGTTTGGAACCCGGAACAATTTCCATGGGTCACATGGT[A/G,GGAGAGGCCAGGTAACAAGTCTCCGGGGTCACATAGGTGGGTCACA]
GAGAGGCCAGGTAACAAGTCTCCGGGGTCACATAGGTTGATGTGACGACTTAAAAGGTGGAACCCGGGTCACATGGTGGAGAGACCAGGTAACAAGTCTT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 52.30% 42.20% 1.27% 4.23% TGTGACCCACCTATGTGACCCCGGAGACTTGTTACCTGGCCTCTCC: 0.02%
All Indica  2759 34.50% 56.20% 2.07% 7.21% NA
All Japonica  1512 95.80% 4.20% 0.00% 0.00% NA
Aus  269 1.50% 98.50% 0.00% 0.00% NA
Indica I  595 4.40% 60.00% 7.06% 28.57% NA
Indica II  465 74.00% 25.60% 0.43% 0.00% NA
Indica III  913 31.00% 67.90% 0.55% 0.55% NA
Indica Intermediate  786 38.20% 57.80% 1.02% 3.05% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 88.50% 11.50% 0.00% 0.00% NA
Japonica Intermediate  241 98.30% 1.70% 0.00% 0.00% NA
VI/Aromatic  96 11.50% 88.50% 0.00% 0.00% NA
Intermediate  90 58.90% 35.60% 3.33% 1.11% TGTGACCCACCTATGTGACCCCGGAGACTTGTTACCTGGCCTCTCC: 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
vg0317005591 T -> C LOC_Os03g29830.1 downstream_gene_variant ; 3279.0bp to feature; MODIFIER silent_mutation Average:72.245; most accessible tissue: Minghui63 panicle, score: 83.421 N N N N
vg0317005591 T -> C LOC_Os03g29850.1 downstream_gene_variant ; 2364.0bp to feature; MODIFIER silent_mutation Average:72.245; most accessible tissue: Minghui63 panicle, score: 83.421 N N N N
vg0317005591 T -> C LOC_Os03g29830-LOC_Os03g29850 intergenic_region ; MODIFIER silent_mutation Average:72.245; most accessible tissue: Minghui63 panicle, score: 83.421 N N N N
vg0317005591 T -> DEL N N silent_mutation Average:72.245; most accessible tissue: Minghui63 panicle, score: 83.421 N N N N
vg0317005591 T -> TGTGACCCACCTATGTGACCCCGGAGACTT GTTACCTGGCCTCTCC LOC_Os03g29830.1 downstream_gene_variant ; 3280.0bp to feature; MODIFIER silent_mutation Average:72.245; most accessible tissue: Minghui63 panicle, score: 83.421 N N N N
vg0317005591 T -> TGTGACCCACCTATGTGACCCCGGAGACTT GTTACCTGGCCTCTCC LOC_Os03g29850.1 downstream_gene_variant ; 2363.0bp to feature; MODIFIER silent_mutation Average:72.245; most accessible tissue: Minghui63 panicle, score: 83.421 N N N N
vg0317005591 T -> TGTGACCCACCTATGTGACCCCGGAGACTT GTTACCTGGCCTCTCC LOC_Os03g29830-LOC_Os03g29850 intergenic_region ; MODIFIER silent_mutation Average:72.245; most accessible tissue: Minghui63 panicle, score: 83.421 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0317005591 5.60E-09 NA Grain_length All YES Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0317005591 2.13E-07 2.48E-33 Grain_length Ind_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0317005591 NA 4.86E-12 Grain_weight All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0317005591 NA 6.19E-07 Grain_weight Ind_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0317005591 NA 6.25E-15 mr1059 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
vg0317005591 NA 4.73E-15 mr1143 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
vg0317005591 NA 9.03E-16 mr1167 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
vg0317005591 NA 7.73E-08 mr1245 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
vg0317005591 NA 2.54E-10 mr1307 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
vg0317005591 NA 2.66E-10 mr1399 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
vg0317005591 NA 7.66E-09 mr1439 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
vg0317005591 NA 5.85E-07 mr1516 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
vg0317005591 NA 6.64E-09 mr1607 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
vg0317005591 NA 4.34E-06 mr1665 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
vg0317005591 NA 9.40E-15 mr1675 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
vg0317005591 NA 1.39E-07 mr1677 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
vg0317005591 NA 1.56E-08 mr1942 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
vg0317005591 NA 1.85E-15 mr1969 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