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Detailed information for vg1126527710:

Variant ID: vg1126527710 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 26527710
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.02, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:


CTATTACGAACAAACATAATAAATGAAGTACATGTTCTTCAACATTATCTTTGAAAGAACTGAGCTGATCATCCTAGTTTGTTAACTCACTAATGCTACC[G/A]
GTGAGTTGTCATATATTCCATGGTAACTTTATATTTAGCGGATATGTACAAGGAAAAAACAGAAGAATATGGATGAATTCCTTTTTCTTTGAAACAGGAT

Reverse complement sequence

ATCCTGTTTCAAAGAAAAAGGAATTCATCCATATTCTTCTGTTTTTTCCTTGTACATATCCGCTAAATATAAAGTTACCATGGAATATATGACAACTCAC[C/T]
GGTAGCATTAGTGAGTTAACAAACTAGGATGATCAGCTCAGTTCTTTCAAAGATAATGTTGAAGAACATGTACTTCATTTATTATGTTTGTTCGTAATAG

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 52.30% 47.50% 0.19% 0.00% NA
All Indica  2759 54.10% 45.70% 0.22% 0.00% NA
All Japonica  1512 53.60% 46.30% 0.13% 0.00% NA
Aus  269 37.90% 62.10% 0.00% 0.00% NA
Indica I  595 51.40% 48.40% 0.17% 0.00% NA
Indica II  465 31.40% 68.40% 0.22% 0.00% NA
Indica III  913 67.60% 32.20% 0.22% 0.00% NA
Indica Intermediate  786 53.80% 45.90% 0.25% 0.00% NA
Temperate Japonica  767 79.50% 20.50% 0.00% 0.00% NA
Tropical Japonica  504 22.60% 77.20% 0.20% 0.00% NA
Japonica Intermediate  241 35.70% 63.90% 0.41% 0.00% NA
VI/Aromatic  96 21.90% 78.10% 0.00% 0.00% NA
Intermediate  90 52.20% 46.70% 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
vg1126527710 G -> A LOC_Os11g43934.1 3_prime_UTR_variant ; 296.0bp to feature; MODIFIER silent_mutation Average:44.589; most accessible tissue: Callus, score: 78.072 N N N N
vg1126527710 G -> A LOC_Os11g43934.2 intron_variant ; MODIFIER silent_mutation Average:44.589; most accessible tissue: Callus, score: 78.072 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1126527710 2.68E-08 NA mr1191 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
vg1126527710 3.11E-07 9.34E-11 mr1191 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
vg1126527710 4.67E-06 8.33E-09 mr1561 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
vg1126527710 1.49E-09 NA mr1644 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
vg1126527710 1.44E-10 8.04E-14 mr1644 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
vg1126527710 5.68E-06 4.18E-07 mr1908 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
vg1126527710 2.22E-11 NA mr1191_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
vg1126527710 4.84E-15 4.44E-20 mr1191_2 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
vg1126527710 NA 2.04E-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
vg1126527710 NA 1.10E-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
vg1126527710 NA 1.48E-06 mr1582_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
vg1126527710 NA 1.23E-06 mr1875_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
vg1126527710 NA 2.41E-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
vg1126527710 NA 7.90E-06 mr1908_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
vg1126527710 NA 1.54E-08 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
vg1126527710 NA 3.56E-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
vg1126527710 NA 8.52E-09 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