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Detailed information for vg1127358883:

Variant ID: vg1127358883 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 27358883
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.01, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:


TCTTCCTTACCAACAAGGCAGGTGAAGACCAAGTACTCTGGCTAGGTTGAATGACCCCTGATGACAACATTTCAGCAACTTGTCTTTCAATCTCATCCTT[G/A]
AGCTCCGGATTGTATCTATAAGGCCTCAGGTTAACTGGTTGGGCTCCCTCTATTAAAGGAATTCTATGATCACAATATCTGGTAGGGGGCAGGCCCCTAG

Reverse complement sequence

CTAGGGGCCTGCCCCCTACCAGATATTGTGATCATAGAATTCCTTTAATAGAGGGAGCCCAACCAGTTAACCTGAGGCCTTATAGATACAATCCGGAGCT[C/T]
AAGGATGAGATTGAAAGACAAGTTGCTGAAATGTTGTCATCAGGGGTCATTCAACCTAGCCAGAGTACTTGGTCTTCACCTGCCTTGTTGGTAAGGAAGA

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 51.70% 23.30% 0.74% 24.29% NA
All Indica  2759 52.30% 32.20% 0.94% 14.50% NA
All Japonica  1512 47.80% 11.70% 0.33% 40.15% NA
Aus  269 61.30% 2.20% 0.37% 36.06% NA
Indica I  595 78.20% 3.70% 0.84% 17.31% NA
Indica II  465 24.50% 72.00% 0.65% 2.80% NA
Indica III  913 53.20% 26.80% 1.10% 18.84% NA
Indica Intermediate  786 48.20% 36.50% 1.02% 14.25% NA
Temperate Japonica  767 66.60% 5.50% 0.26% 27.64% NA
Tropical Japonica  504 22.40% 16.30% 0.40% 60.91% NA
Japonica Intermediate  241 41.10% 22.00% 0.41% 36.51% NA
VI/Aromatic  96 70.80% 4.20% 1.04% 23.96% NA
Intermediate  90 47.80% 26.70% 2.22% 23.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1127358883 G -> A LOC_Os11g45200.1 synonymous_variant ; p.Leu521Leu; LOW synonymous_codon Average:41.818; most accessible tissue: Minghui63 young leaf, score: 65.161 N N N N
vg1127358883 G -> DEL LOC_Os11g45200.1 N frameshift_variant Average:41.818; most accessible tissue: Minghui63 young leaf, score: 65.161 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1127358883 NA 3.11E-06 mr1138 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
vg1127358883 NA 4.26E-06 mr1169 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
vg1127358883 NA 8.85E-06 mr1185 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
vg1127358883 NA 1.24E-06 mr1212 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
vg1127358883 NA 6.14E-06 mr1291 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
vg1127358883 NA 1.52E-07 mr1557 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
vg1127358883 NA 1.37E-06 mr1742 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
vg1127358883 NA 4.38E-06 mr1745 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
vg1127358883 NA 8.37E-07 mr1928 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
vg1127358883 NA 9.58E-06 mr1975 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
vg1127358883 3.00E-06 NA mr1042_2 Jap_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
vg1127358883 NA 4.45E-07 mr1232_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
vg1127358883 NA 2.44E-06 mr1238_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
vg1127358883 NA 1.86E-06 mr1380_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
vg1127358883 NA 5.24E-10 mr1380_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
vg1127358883 NA 3.02E-06 mr1497_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
vg1127358883 NA 3.17E-09 mr1557_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
vg1127358883 NA 5.79E-09 mr1561_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
vg1127358883 NA 2.63E-09 mr1598_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
vg1127358883 NA 1.26E-07 mr1609_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
vg1127358883 NA 1.31E-07 mr1745_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
vg1127358883 2.93E-07 NA mr1871_2 Jap_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
vg1127358883 NA 1.09E-08 mr1875_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
vg1127358883 NA 4.77E-07 mr1900_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
vg1127358883 NA 2.04E-07 mr1908_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
vg1127358883 NA 6.66E-06 mr1931_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
vg1127358883 NA 1.57E-06 mr1977_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
vg1127358883 NA 8.30E-06 mr1996_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
vg1127358883 NA 2.25E-07 mr1996_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