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Detailed information for vg0528383107:

Variant ID: vg0528383107 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 28383107
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, A: 0.02, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:


GATGATGCGATCATTGAACGTAGGCTTCTGACCAGGACAACAACTACCAGGAGTGAACCACCACTAAGGACAACATAGGCTGTGTTTAGAGGGTGTTTGG[G/A]
AAGTAGGGACTAAACTTTAGTCCCTCTCACAAAAGCATAAGGGGGTGTTTGGGAACTAGGGACTAAATTTAGTCCCTCTCACAAAAATATAAGTCCCTTT

Reverse complement sequence

AAAGGGACTTATATTTTTGTGAGAGGGACTAAATTTAGTCCCTAGTTCCCAAACACCCCCTTATGCTTTTGTGAGAGGGACTAAAGTTTAGTCCCTACTT[C/T]
CCAAACACCCTCTAAACACAGCCTATGTTGTCCTTAGTGGTGGTTCACTCCTGGTAGTTGTTGTCCTGGTCAGAAGCCTACGTTCAATGATCGCATCATC

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 90.60% 7.80% 1.65% 0.00% NA
All Indica  2759 99.70% 0.30% 0.00% 0.00% NA
All Japonica  1512 71.80% 23.20% 4.96% 0.00% NA
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 98.50% 1.50% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 53.10% 38.50% 8.47% 0.00% NA
Tropical Japonica  504 99.20% 0.60% 0.20% 0.00% NA
Japonica Intermediate  241 74.30% 22.00% 3.73% 0.00% NA
VI/Aromatic  96 91.70% 6.20% 2.08% 0.00% NA
Intermediate  90 96.70% 2.20% 1.11% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0528383107 G -> A LOC_Os05g49490.1 downstream_gene_variant ; 4166.0bp to feature; MODIFIER silent_mutation Average:54.127; most accessible tissue: Minghui63 panicle, score: 76.913 N N N N
vg0528383107 G -> A LOC_Os05g49500.1 downstream_gene_variant ; 1471.0bp to feature; MODIFIER silent_mutation Average:54.127; most accessible tissue: Minghui63 panicle, score: 76.913 N N N N
vg0528383107 G -> A LOC_Os05g49490-LOC_Os05g49500 intergenic_region ; MODIFIER silent_mutation Average:54.127; most accessible tissue: Minghui63 panicle, score: 76.913 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0528383107 NA 1.41E-12 Heading_date 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
vg0528383107 NA 2.53E-13 Heading_date Jap_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
vg0528383107 NA 9.57E-06 mr1126 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
vg0528383107 NA 1.71E-06 mr1252 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
vg0528383107 NA 1.04E-06 mr1252 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
vg0528383107 NA 1.44E-06 mr1045_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
vg0528383107 6.03E-06 2.43E-10 mr1567_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
vg0528383107 NA 2.10E-07 mr1567_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
vg0528383107 NA 1.40E-06 mr1588_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
vg0528383107 NA 3.01E-07 mr1671_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
vg0528383107 NA 5.57E-07 mr1680_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
vg0528383107 3.28E-06 NA mr1806_2 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
vg0528383107 NA 1.34E-10 mr1829_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
vg0528383107 NA 2.04E-17 mr1902_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
vg0528383107 NA 3.60E-06 mr1902_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