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Detailed information for vg1126586105:

Variant ID: vg1126586105 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 26586105
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 57. )

Flanking Sequence (100 bp) in Reference Genome:


TCCAAAAAAAGTACCTCGAGGTATCGGTACTTCACGGTACTAAATAGTTTCCGATCTTTGGATTTAGCTGTACAGGATGGGCATTGTTAGATCTAATGAT[C/T]
GGAAGCAATTTGGTACCGTGAGATTCTGGTACCTCGAGGTACTTTTTTTTTTTTACCGGAACTACTCATCTGGATAACATGCATATCCTCAGGATTGGAT

Reverse complement sequence

ATCCAATCCTGAGGATATGCATGTTATCCAGATGAGTAGTTCCGGTAAAAAAAAAAAAGTACCTCGAGGTACCAGAATCTCACGGTACCAAATTGCTTCC[G/A]
ATCATTAGATCTAACAATGCCCATCCTGTACAGCTAAATCCAAAGATCGGAAACTATTTAGTACCGTGAAGTACCGATACCTCGAGGTACTTTTTTTGGA

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 86.10% 12.80% 0.11% 0.97% NA
All Indica  2759 79.00% 19.10% 0.18% 1.67% NA
All Japonica  1512 99.20% 0.80% 0.00% 0.00% NA
Aus  269 84.00% 16.00% 0.00% 0.00% NA
Indica I  595 64.00% 30.10% 0.50% 5.38% NA
Indica II  465 81.70% 18.10% 0.00% 0.22% NA
Indica III  913 83.70% 16.20% 0.00% 0.11% NA
Indica Intermediate  786 83.30% 14.90% 0.25% 1.53% NA
Temperate Japonica  767 98.70% 1.30% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 95.80% 4.20% 0.00% 0.00% NA
Intermediate  90 78.90% 21.10% 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
vg1126586105 C -> T LOC_Os11g43990.1 upstream_gene_variant ; 3920.0bp to feature; MODIFIER silent_mutation Average:45.552; most accessible tissue: Zhenshan97 young leaf, score: 66.32 N N N N
vg1126586105 C -> T LOC_Os11g44014.1 downstream_gene_variant ; 1221.0bp to feature; MODIFIER silent_mutation Average:45.552; most accessible tissue: Zhenshan97 young leaf, score: 66.32 N N N N
vg1126586105 C -> T LOC_Os11g44000.1 intron_variant ; MODIFIER silent_mutation Average:45.552; most accessible tissue: Zhenshan97 young leaf, score: 66.32 N N N N
vg1126586105 C -> DEL N N silent_mutation Average:45.552; most accessible tissue: Zhenshan97 young leaf, score: 66.32 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1126586105 NA 8.90E-13 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
vg1126586105 NA 7.11E-10 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
vg1126586105 NA 2.75E-06 mr1295 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
vg1126586105 NA 1.71E-06 mr1295 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
vg1126586105 NA 1.05E-06 mr1561 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
vg1126586105 NA 2.28E-13 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
vg1126586105 NA 5.97E-11 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
vg1126586105 3.30E-07 9.32E-09 mr1662 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
vg1126586105 6.56E-06 2.54E-07 mr1662 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
vg1126586105 NA 1.74E-06 mr1908 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
vg1126586105 1.13E-06 2.25E-19 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
vg1126586105 1.29E-07 3.49E-15 mr1191_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
vg1126586105 9.30E-06 5.16E-08 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
vg1126586105 6.02E-07 5.72E-08 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
vg1126586105 2.90E-06 3.77E-09 mr1561_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
vg1126586105 5.06E-07 3.36E-08 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
vg1126586105 NA 3.86E-07 mr1662_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
vg1126586105 NA 2.90E-06 mr1662_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
vg1126586105 NA 5.97E-06 mr1745_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
vg1126586105 1.45E-06 2.22E-10 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
vg1126586105 6.11E-07 7.30E-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
vg1126586105 1.89E-06 3.24E-10 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
vg1126586105 1.40E-06 6.84E-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
vg1126586105 6.95E-06 3.01E-07 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
vg1126586105 4.88E-06 1.88E-06 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