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Detailed information for vg0505372955:

Variant ID: vg0505372955 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 5372955
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.64, G: 0.37, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:


TTGGCAGATGCCAGGAAAGAAAAGAAAAGTCAATCCATGACTCAAATCTGGCTTTAAATTTCTTCTCCAAAAAGAATCAAAAGGCTGAATTTCCTGAAAA[A/G]
TCTTAAATCACACCGTAAAGTCTTAAAAAACAGAGGACGAAGATAACATCATGCAAAATCGTGATGCTGGTGCTATGTTGTCAATATCACACACTTTCAT

Reverse complement sequence

ATGAAAGTGTGTGATATTGACAACATAGCACCAGCATCACGATTTTGCATGATGTTATCTTCGTCCTCTGTTTTTTAAGACTTTACGGTGTGATTTAAGA[T/C]
TTTTCAGGAAATTCAGCCTTTTGATTCTTTTTGGAGAAGAAATTTAAAGCCAGATTTGAGTCATGGATTGACTTTTCTTTTCTTTCCTGGCATCTGCCAA

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 56.40% 43.40% 0.21% 0.00% NA
All Indica  2759 49.10% 50.70% 0.11% 0.00% NA
All Japonica  1512 73.30% 26.30% 0.40% 0.00% NA
Aus  269 22.70% 77.30% 0.00% 0.00% NA
Indica I  595 85.20% 14.60% 0.17% 0.00% NA
Indica II  465 22.80% 76.80% 0.43% 0.00% NA
Indica III  913 40.00% 60.00% 0.00% 0.00% NA
Indica Intermediate  786 48.10% 51.90% 0.00% 0.00% NA
Temperate Japonica  767 92.70% 6.50% 0.78% 0.00% NA
Tropical Japonica  504 44.80% 55.20% 0.00% 0.00% NA
Japonica Intermediate  241 71.00% 29.00% 0.00% 0.00% NA
VI/Aromatic  96 90.60% 8.30% 1.04% 0.00% NA
Intermediate  90 58.90% 41.10% 0.00% 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
vg0505372955 A -> G LOC_Os05g09520-LOC_Os05g09530 intergenic_region ; MODIFIER silent_mutation Average:41.504; most accessible tissue: Callus, score: 62.83 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0505372955 NA 5.73E-21 Grain_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
vg0505372955 NA 1.47E-15 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
vg0505372955 5.34E-13 NA Grain_thickness 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
vg0505372955 6.65E-08 1.71E-14 Grain_thickness 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
vg0505372955 2.18E-06 5.96E-15 Grain_thickness 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
vg0505372955 2.20E-23 NA Grain_width 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
vg0505372955 5.96E-18 1.14E-33 Grain_width 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
vg0505372955 2.42E-10 6.42E-18 Grain_width 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
vg0505372955 NA 5.85E-08 mr1183 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
vg0505372955 NA 1.30E-07 mr1503 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
vg0505372955 NA 2.78E-08 mr1593 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
vg0505372955 NA 2.32E-07 mr1733 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
vg0505372955 NA 7.84E-13 mr1769 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
vg0505372955 NA 1.18E-07 mr1183_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
vg0505372955 NA 1.19E-06 mr1319_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
vg0505372955 NA 1.36E-06 mr1330_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
vg0505372955 NA 1.35E-09 mr1771_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
vg0505372955 NA 9.46E-06 mr1959_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