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Detailed information for vg0710993399:

Variant ID: vg0710993399 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 10993399
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.75, A: 0.25, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:


TCAAATCGAAGGCTCATGAACTCAGGGAGGTTTCAGCTGCTATGCTACGTACCTGAATAATTACAGTTCCAAGATCAAGTTTGGTGATTTTGTCGGACAG[G/A]
TAGCCCAATACCTTCAGTTGAGGCGCCCTGACCACCCTGACATTCTTTGGGCCACTGTGCGGATCGAGCAACATCAATCTCTCGAGGCATGGTGCATCCT

Reverse complement sequence

AGGATGCACCATGCCTCGAGAGATTGATGTTGCTCGATCCGCACAGTGGCCCAAAGAATGTCAGGGTGGTCAGGGCGCCTCAACTGAAGGTATTGGGCTA[C/T]
CTGTCCGACAAAATCACCAAACTTGATCTTGGAACTGTAATTATTCAGGTACGTAGCATAGCAGCTGAAACCTCCCTGAGTTCATGAGCCTTCGATTTGA

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% 9.40% 0.02% 0.00% NA
All Indica  2759 97.80% 2.10% 0.04% 0.00% NA
All Japonica  1512 80.50% 19.50% 0.00% 0.00% NA
Aus  269 95.20% 4.80% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 92.60% 7.30% 0.13% 0.00% NA
Temperate Japonica  767 67.00% 33.00% 0.00% 0.00% NA
Tropical Japonica  504 99.40% 0.60% 0.00% 0.00% NA
Japonica Intermediate  241 83.80% 16.20% 0.00% 0.00% NA
VI/Aromatic  96 24.00% 76.00% 0.00% 0.00% NA
Intermediate  90 95.60% 4.40% 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
vg0710993399 G -> A LOC_Os07g18600.1 synonymous_variant ; p.Tyr292Tyr; LOW synonymous_codon Average:64.176; most accessible tissue: Zhenshan97 young leaf, score: 82.982 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0710993399 NA 1.73E-26 Awn_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
vg0710993399 NA 7.72E-08 Awn_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
vg0710993399 NA 4.60E-09 mr1624 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
vg0710993399 NA 2.89E-08 mr1624_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
vg0710993399 NA 5.57E-06 mr1741_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