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Detailed information for vg0710993182:

Variant ID: vg0710993182 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 10993182
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CACCATGATGTACAGCTTCTCCAAGCATGGAAAACATTTAAGGAAGCCAAATTGTGTCCAGATTTGGTCCAGCAGACTCAAGAACCAAAACCTTCACTGT[G/A]
CGCAGCGAGGCTGTCGAACTGACGACCATCGTTTCCTGAAGAAAACCAAGACGTACAGCATGTCAAGATGTCCATGTCCAAATTCACAACATATACTGAT

Reverse complement sequence

ATCAGTATATGTTGTGAATTTGGACATGGACATCTTGACATGCTGTACGTCTTGGTTTTCTTCAGGAAACGATGGTCGTCAGTTCGACAGCCTCGCTGCG[C/T]
ACAGTGAAGGTTTTGGTTCTTGAGTCTGCTGGACCAAATCTGGACACAATTTGGCTTCCTTAAATGTTTTCCATGCTTGGAGAAGCTGTACATCATGGTG

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% 0.00% 0.00% NA
All Indica  2759 97.90% 2.10% 0.00% 0.00% NA
All Japonica  1512 80.60% 19.40% 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 92.70% 7.30% 0.00% 0.00% NA
Temperate Japonica  767 67.10% 32.90% 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 22.90% 77.10% 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
vg0710993182 G -> A LOC_Os07g18600.1 synonymous_variant ; p.Arg320Arg; LOW synonymous_codon Average:47.681; most accessible tissue: Callus, score: 88.323 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0710993182 NA 9.39E-24 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
vg0710993182 NA 2.02E-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
vg0710993182 NA 9.08E-09 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
vg0710993182 NA 2.33E-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
vg0710993182 NA 5.73E-06 mr1887_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