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Detailed information for vg1122650141:

Variant ID: vg1122650141 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 22650141
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, A: 0.00, others allele: 0.00, population size: 272. )

Flanking Sequence (100 bp) in Reference Genome:


TGACGGCATTCGTCGAAAAGGGGAAGCTGAAGAAGATTGCAGGGGTGAAGACCAAAGAGCTGATGCTGTGGCTCAGTGTGGTTGAGGTCTATGTTGATGA[G/A]
TCTTCTGCTGGGAAGATCACATTCAAGACTGGCACTGGCCTCTCCGATAGTTTTGATGCGTCGGCCTTCGAGTTAGGAATGTAAACTGAAGAACATATCA

Reverse complement sequence

TGATATGTTCTTCAGTTTACATTCCTAACTCGAAGGCCGACGCATCAAAACTATCGGAGAGGCCAGTGCCAGTCTTGAATGTGATCTTCCCAGCAGAAGA[C/T]
TCATCAACATAGACCTCAACCACACTGAGCCACAGCATCAGCTCTTTGGTCTTCACCCCTGCAATCTTCTTCAGCTTCCCCTTTTCGACGAATGCCGTCA

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 77.30% 22.50% 0.02% 0.19% NA
All Indica  2759 99.10% 0.90% 0.00% 0.00% NA
All Japonica  1512 31.70% 67.70% 0.00% 0.60% NA
Aus  269 98.90% 1.10% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 98.90% 1.10% 0.00% 0.00% NA
Indica Intermediate  786 98.50% 1.50% 0.00% 0.00% NA
Temperate Japonica  767 38.30% 61.70% 0.00% 0.00% NA
Tropical Japonica  504 21.20% 77.20% 0.00% 1.59% NA
Japonica Intermediate  241 32.80% 66.80% 0.00% 0.41% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 84.40% 14.40% 1.11% 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
vg1122650141 G -> A LOC_Os11g38210.1 synonymous_variant ; p.Glu115Glu; LOW synonymous_codon Average:54.749; most accessible tissue: Zhenshan97 flower, score: 68.001 N N N N
vg1122650141 G -> DEL LOC_Os11g38210.1 N frameshift_variant Average:54.749; most accessible tissue: Zhenshan97 flower, score: 68.001 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1122650141 NA 2.75E-06 mr1028 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
vg1122650141 2.73E-06 NA mr1071 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
vg1122650141 1.35E-07 NA mr1140 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
vg1122650141 5.31E-07 NA mr1203 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
vg1122650141 NA 1.38E-28 mr1238 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
vg1122650141 8.65E-06 1.43E-30 mr1309 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
vg1122650141 2.26E-06 NA mr1395 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
vg1122650141 NA 1.11E-18 mr1484 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
vg1122650141 3.87E-07 NA mr1618 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
vg1122650141 NA 6.26E-13 mr1641 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
vg1122650141 NA 1.60E-14 mr1900 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
vg1122650141 NA 2.32E-10 mr1921 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
vg1122650141 1.42E-06 1.23E-31 mr1238_2 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
vg1122650141 7.22E-07 1.60E-29 mr1484_2 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
vg1122650141 1.90E-06 2.14E-33 mr1841_2 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
vg1122650141 9.88E-06 3.35E-23 mr1900_2 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
vg1122650141 NA 1.89E-19 mr1945_2 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