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Detailed information for vg0710994254:

Variant ID: vg0710994254 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 10994254
Reference Allele: TAlternative Allele: G
Primary Allele: TSecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CGGGGAGGACGCTGATCAGGTCGATGCCCCCCGCATCAGCATCGCCTCCCTCCGATCGTTCTTGGCAATCCGGTTCGTCGTGTCTCCGTTTCTTGGCGAC[T/G]
GGAGCGGTCACCTCTTCCATGGCCGGCGGTAGGCCGTGGGCGGCGTGAGAGGTGGCGGTTGTGTTGATGAGAAATTGAGAAGCGAGTCGGTTGTGGTTTT

Reverse complement sequence

AAAACCACAACCGACTCGCTTCTCAATTTCTCATCAACACAACCGCCACCTCTCACGCCGCCCACGGCCTACCGCCGGCCATGGAAGAGGTGACCGCTCC[A/C]
GTCGCCAAGAAACGGAGACACGACGAACCGGATTGCCAAGAACGATCGGAGGGAGGCGATGCTGATGCGGGGGGCATCGACCTGATCAGCGTCCTCCCCG

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of G(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 97.90% 2.10% 0.00% 0.00% NA
All Japonica  1512 80.50% 19.40% 0.07% 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 67.00% 32.90% 0.13% 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
vg0710994254 T -> G LOC_Os07g18600.1 synonymous_variant ; p.Pro7Pro; LOW synonymous_codon Average:72.246; most accessible tissue: Minghui63 flag leaf, score: 87.052 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0710994254 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
vg0710994254 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
vg0710994254 NA 8.23E-10 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
vg0710994254 NA 3.63E-06 mr1062_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
vg0710994254 NA 6.05E-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
vg0710994254 NA 3.03E-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
vg0710994254 NA 5.15E-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