Variant ID: vg1013546417 (JBrowse) | Variation Type: SNP |
Chromosome: chr10 | Position: 13546417 |
Reference Allele: A | Alternative Allele: T |
Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 259. )
CAACTGCTGATCGGGTATATGAACATCCAATTAGTAGACTTTTTTTTCTCTTTTTATATAATTATTAACTTAAGAGGTATGTCCCATCATTACAGATATT[A/T]
TACTGGAAGATAGTTCCATCTACTCCAGCTGGACCTCCGAACTCTGATCCTGTAAATGATGGACCTGTTTTATCAGTTCGATATTCCCTGGATCTGAAAG
CTTTCAGATCCAGGGAATATCGAACTGATAAAACAGGTCCATCATTTACAGGATCAGAGTTCGGAGGTCCAGCTGGAGTAGATGGAACTATCTTCCAGTA[T/A]
AATATCTGTAATGATGGGACATACCTCTTAAGTTAATAATTATATAAAAAGAGAAAAAAAAGTCTACTAATTGGATGTTCATATACCCGATCAGCAGTTG
Populations | Population Size | Frequency 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 |
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 |
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 |