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Detailed information for vg0809213665:

Variant ID: vg0809213665 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 9213665
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.82, A: 0.18, others allele: 0.00, population size: 66. )

Flanking Sequence (100 bp) in Reference Genome:


ATGCCCGATGGGCACCGCGGAGAAGAATATCACCAGGGTTTTGACTCTGGAGCCAACTCGGTTCAGGATCGAACCCTGGTCAAGGGTAAGCCGATTTTTC[A/G]
CAACTCGCCAGTTAATTTTGATTTGTGGGAGAATTCTAAGAGTGGGGCTTTGGGATTCCAGAGTGGTGGACGAGCCGGAAATTCTAGGTTGCCTAAGTCT

Reverse complement sequence

AGACTTAGGCAACCTAGAATTTCCGGCTCGTCCACCACTCTGGAATCCCAAAGCCCCACTCTTAGAATTCTCCCACAAATCAAAATTAACTGGCGAGTTG[T/C]
GAAAAATCGGCTTACCCTTGACCAGGGTTCGATCCTGAACCGAGTTGGCTCCAGAGTCAAAACCCTGGTGATATTCTTCTCCGCGGTGCCCATCGGGCAT

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 51.00% 15.70% 0.83% 32.48% NA
All Indica  2759 70.70% 7.80% 0.76% 20.77% NA
All Japonica  1512 9.30% 33.60% 0.73% 56.35% NA
Aus  269 98.90% 0.00% 0.74% 0.37% NA
Indica I  595 58.20% 21.00% 1.34% 19.50% NA
Indica II  465 46.50% 3.90% 1.51% 48.17% NA
Indica III  913 92.60% 0.20% 0.11% 7.12% NA
Indica Intermediate  786 69.20% 8.80% 0.64% 21.37% NA
Temperate Japonica  767 1.70% 57.60% 0.39% 40.29% NA
Tropical Japonica  504 20.80% 1.40% 1.19% 76.59% NA
Japonica Intermediate  241 9.50% 24.50% 0.83% 65.15% NA
VI/Aromatic  96 14.60% 0.00% 2.08% 83.33% NA
Intermediate  90 44.40% 20.00% 3.33% 32.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0809213665 A -> G LOC_Os08g15220.1 missense_variant ; p.His107Arg; MODERATE nonsynonymous_codon ; H107R Average:61.884; most accessible tissue: Minghui63 flag leaf, score: 82.75 unknown unknown TOLERATED 0.35
vg0809213665 A -> DEL LOC_Os08g15220.1 N frameshift_variant Average:61.884; most accessible tissue: Minghui63 flag leaf, score: 82.75 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0809213665 NA 6.90E-21 Heading_date 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
vg0809213665 NA 1.87E-14 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
vg0809213665 NA 1.49E-12 Plant_height 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
vg0809213665 NA 2.18E-17 Spikelet_length 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
vg0809213665 NA 1.22E-12 Spikelet_length 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
vg0809213665 NA 4.29E-06 mr1325 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
vg0809213665 NA 8.65E-06 mr1532 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
vg0809213665 NA 3.61E-06 mr1011_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
vg0809213665 NA 4.68E-06 mr1060_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
vg0809213665 NA 4.83E-06 mr1129_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
vg0809213665 NA 1.99E-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
vg0809213665 NA 3.68E-06 mr1919_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