| Variant ID: vg1217487071 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 17487071 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 350. )
AGGCTAGAAGATGGACATTATACCTTGATGAGGAGCAAGTGAAGACATTGATGATGCGGGGTATGAAGTGGCTATTTATGGCAAAACGGTGAAGGGCAAG[C/T]
AAGGCTCGGCTACAATGGACCATGCGGGGAGAGGCTTGGCACCGATGGACCGAATCCGGTAGTGAAAGGCGAGTGAAGGCTTTGTCATGATGGTCATGAT
ATCATGACCATCATGACAAAGCCTTCACTCGCCTTTCACTACCGGATTCGGTCCATCGGTGCCAAGCCTCTCCCCGCATGGTCCATTGTAGCCGAGCCTT[G/A]
CTTGCCCTTCACCGTTTTGCCATAAATAGCCACTTCATACCCCGCATCATCAATGTCTTCACTTGCTCCTCATCAAGGTATAATGTCCATCTTCTAGCCT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 95.90% | 3.20% | 0.78% | 0.08% | NA |
| All Indica | 2759 | 99.30% | 0.60% | 0.07% | 0.00% | NA |
| All Japonica | 1512 | 97.70% | 0.00% | 2.05% | 0.26% | NA |
| Aus | 269 | 49.10% | 49.80% | 1.12% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 98.20% | 1.50% | 0.25% | 0.00% | NA |
| Temperate Japonica | 767 | 95.60% | 0.00% | 3.91% | 0.52% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 98.90% | 0.00% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1217487071 | C -> DEL | LOC_Os12g29434.1 | N | frameshift_variant | Average:42.124; most accessible tissue: Minghui63 flag leaf, score: 57.881 | N | N | N | N |
| vg1217487071 | C -> T | LOC_Os12g29434.1 | stop_gained ; p.Gln306*; HIGH | stop_gained | Average:42.124; most accessible tissue: Minghui63 flag leaf, score: 57.881 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1217487071 | 8.89E-06 | NA | mr1368 | 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 |
| vg1217487071 | NA | 9.76E-08 | mr1762_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 |