| Variant ID: vg0805496353 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 5496353 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
CTACCCTTGCCGCACTCGCTCGCTCTCAAGCTCCTCCTCCGCCGGCGTCATGGCACGGGGCTCCGTACCGCTCGACGGTAGCGTGCTGCCGCCTTCCCGC[A/C]
TCGTGAGCGAGAGGCAGGCCGGGCTGCCGCGCCGATTCATGCCGGAATCTGCCACCGGCCGGGAGGTGGTCGCGCTGGGCAAGGGACGCCCGGCGCCACA
TGTGGCGCCGGGCGTCCCTTGCCCAGCGCGACCACCTCCCGGCCGGTGGCAGATTCCGGCATGAATCGGCGCGGCAGCCCGGCCTGCCTCTCGCTCACGA[T/G]
GCGGGAAGGCGGCAGCACGCTACCGTCGAGCGGTACGGAGCCCCGTGCCATGACGCCGGCGGAGGAGGAGCTTGAGAGCGAGCGAGTGCGGCAAGGGTAG
| Populations | Population Size | Frequency of A(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 70.70% | 1.10% | 5.78% | 22.51% | NA |
| All Indica | 2759 | 60.10% | 1.70% | 7.43% | 30.70% | NA |
| All Japonica | 1512 | 90.10% | 0.00% | 0.60% | 9.33% | NA |
| Aus | 269 | 74.70% | 0.40% | 16.36% | 8.55% | NA |
| Indica I | 595 | 56.00% | 2.70% | 10.92% | 30.42% | NA |
| Indica II | 465 | 35.30% | 1.50% | 6.67% | 56.56% | NA |
| Indica III | 913 | 78.10% | 1.10% | 4.49% | 16.32% | NA |
| Indica Intermediate | 786 | 57.10% | 1.90% | 8.65% | 32.32% | NA |
| Temperate Japonica | 767 | 96.60% | 0.00% | 0.52% | 2.87% | NA |
| Tropical Japonica | 504 | 84.30% | 0.00% | 0.79% | 14.88% | NA |
| Japonica Intermediate | 241 | 81.30% | 0.00% | 0.41% | 18.26% | NA |
| VI/Aromatic | 96 | 59.40% | 0.00% | 11.46% | 29.17% | NA |
| Intermediate | 90 | 66.70% | 1.10% | 4.44% | 27.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0805496353 | A -> C | LOC_Os08g09490.1 | missense_variant ; p.His27Pro; MODERATE | nonsynonymous_codon ; H27P | Average:43.231; most accessible tissue: Zhenshan97 flag leaf, score: 82.703 | unknown | unknown | DELETERIOUS | 0.00 |
| vg0805496353 | A -> DEL | LOC_Os08g09490.1 | N | frameshift_variant | Average:43.231; most accessible tissue: Zhenshan97 flag leaf, score: 82.703 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0805496353 | NA | 7.40E-06 | mr1402 | 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 |
| vg0805496353 | NA | 7.09E-06 | mr1895 | 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 |