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Detailed information for vg1127176280:

Variant ID: vg1127176280 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 27176280
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:


GCTGCTATTCATCCTTGTCATGGATACCTTTGCGGCGATGTGTGCGACGGCTCTTCAAAGGGGCGCGCTCTCCCCGCTTGCTAGAGATTTGCTGCCGCTG[C/T]
GAGTGTCCCTATATGCGGATGATGCAATCGTTTTCTTTTACCCCTCCACACAAGACGCTGCCGTCATCCAGTTCATTCTCAACCTTTTGGGAGCTGCTAC

Reverse complement sequence

GTAGCAGCTCCCAAAAGGTTGAGAATGAACTGGATGACGGCAGCGTCTTGTGTGGAGGGGTAAAAGAAAACGATTGCATCATCCGCATATAGGGACACTC[G/A]
CAGCGGCAGCAAATCTCTAGCAAGCGGGGAGAGCGCGCCCCTTTGAAGAGCCGTCGCACACATCGCCGCAAAGGTATCCATGACAAGGATGAATAGCAGC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 85.80% 14.10% 0.04% 0.00% NA
All Indica  2759 83.50% 16.50% 0.00% 0.00% NA
All Japonica  1512 93.80% 6.20% 0.07% 0.00% NA
Aus  269 78.40% 21.20% 0.37% 0.00% NA
Indica I  595 75.00% 25.00% 0.00% 0.00% NA
Indica II  465 97.80% 2.20% 0.00% 0.00% NA
Indica III  913 85.30% 14.70% 0.00% 0.00% NA
Indica Intermediate  786 79.50% 20.50% 0.00% 0.00% NA
Temperate Japonica  767 93.60% 6.30% 0.13% 0.00% NA
Tropical Japonica  504 97.40% 2.60% 0.00% 0.00% NA
Japonica Intermediate  241 86.70% 13.30% 0.00% 0.00% NA
VI/Aromatic  96 42.70% 57.30% 0.00% 0.00% NA
Intermediate  90 90.00% 10.00% 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
vg1127176280 C -> T LOC_Os11g44900.1 stop_gained ; p.Arg271*; HIGH stop_gained Average:62.957; most accessible tissue: Callus, score: 83.77 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1127176280 6.18E-06 1.63E-06 mr1206 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
vg1127176280 NA 3.28E-06 mr1314 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
vg1127176280 1.05E-07 1.95E-08 mr1376 Ind_All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1127176280 1.05E-07 1.95E-08 mr1431 Ind_All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1127176280 NA 1.43E-07 mr1542 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
vg1127176280 8.91E-08 9.14E-08 mr1775 Ind_All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1127176280 6.83E-06 1.24E-06 mr1820 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
vg1127176280 NA 8.23E-09 mr1542_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