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Detailed information for vg1013546417:

Variant ID: vg1013546417 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 13546417
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:


CAACTGCTGATCGGGTATATGAACATCCAATTAGTAGACTTTTTTTTCTCTTTTTATATAATTATTAACTTAAGAGGTATGTCCCATCATTACAGATATT[A/T]
TACTGGAAGATAGTTCCATCTACTCCAGCTGGACCTCCGAACTCTGATCCTGTAAATGATGGACCTGTTTTATCAGTTCGATATTCCCTGGATCTGAAAG

Reverse complement sequence

CTTTCAGATCCAGGGAATATCGAACTGATAAAACAGGTCCATCATTTACAGGATCAGAGTTCGGAGGTCCAGCTGGAGTAGATGGAACTATCTTCCAGTA[T/A]
AATATCTGTAATGATGGGACATACCTCTTAAGTTAATAATTATATAAAAAGAGAAAAAAAAGTCTACTAATTGGATGTTCATATACCCGATCAGCAGTTG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 82.00% 17.70% 0.21% 0.11% NA
All Indica  2759 69.90% 29.60% 0.29% 0.18% NA
All Japonica  1512 99.50% 0.50% 0.00% 0.00% NA
Aus  269 98.50% 1.50% 0.00% 0.00% NA
Indica I  595 69.10% 30.30% 0.50% 0.17% NA
Indica II  465 88.80% 11.20% 0.00% 0.00% NA
Indica III  913 63.40% 36.10% 0.22% 0.22% NA
Indica Intermediate  786 66.90% 32.40% 0.38% 0.25% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 98.60% 1.40% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 87.80% 10.00% 2.22% 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
vg1013546417 A -> T LOC_Os10g26140.1 missense_variant ; p.Leu49Phe; MODERATE nonsynonymous_codon ; L49F Average:52.776; most accessible tissue: Zhenshan97 young leaf, score: 73.147 unknown unknown TOLERATED 1.00
vg1013546417 A -> T LOC_Os10g26145.1 missense_variant ; p.Leu59Phe; MODERATE nonsynonymous_codon ; L59F Average:52.776; most accessible tissue: Zhenshan97 young leaf, score: 73.147 unknown unknown TOLERATED 1.00
vg1013546417 A -> T LOC_Os10g26140.3 missense_variant ; p.Leu49Phe; MODERATE nonsynonymous_codon ; L49F Average:52.776; most accessible tissue: Zhenshan97 young leaf, score: 73.147 unknown unknown TOLERATED 1.00
vg1013546417 A -> T LOC_Os10g26140.2 missense_variant ; p.Leu49Phe; MODERATE nonsynonymous_codon ; L49F Average:52.776; most accessible tissue: Zhenshan97 young leaf, score: 73.147 unknown unknown TOLERATED 1.00
vg1013546417 A -> DEL LOC_Os10g26140.1 N frameshift_variant Average:52.776; most accessible tissue: Zhenshan97 young leaf, score: 73.147 N N N N
vg1013546417 A -> DEL LOC_Os10g26140.2 N frameshift_variant Average:52.776; most accessible tissue: Zhenshan97 young leaf, score: 73.147 N N N N
vg1013546417 A -> DEL LOC_Os10g26140.3 N frameshift_variant Average:52.776; most accessible tissue: Zhenshan97 young leaf, score: 73.147 N N N N
vg1013546417 A -> DEL LOC_Os10g26145.1 N frameshift_variant Average:52.776; most accessible tissue: Zhenshan97 young leaf, score: 73.147 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1013546417 3.34E-22 NA mr1533 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
vg1013546417 6.07E-23 3.87E-31 mr1533 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
vg1013546417 NA 1.59E-07 mr1667 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
vg1013546417 8.36E-27 NA mr1980 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
vg1013546417 6.39E-27 1.42E-35 mr1980 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
vg1013546417 6.87E-25 NA mr1533_2 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
vg1013546417 2.59E-28 2.11E-38 mr1533_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
vg1013546417 5.99E-09 NA mr1980_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
vg1013546417 4.08E-10 1.44E-14 mr1980_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