| Variant ID: vg1007738693 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 7738693 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 236. )
TTGGAAGAACTCCCTGAGGCAGTAGTGTTTGCTGCTGGCCTCTTTCCCTTGCCCCGGTCTGCTGCCGTTGGGGGTGGAGTTGGAGGTGGTGGTCTATAAG[C/T]
AGCAGCGAGCTGCGCCATGTCGATGGTCTGCCACTGAACTGCTCCTTGCGGTGCCTGTGGGGCTGCCCCTGCGACGGCGGAGTGGTTTCCGACAACTGTG
CACAGTTGTCGGAAACCACTCCGCCGTCGCAGGGGCAGCCCCACAGGCACCGCAAGGAGCAGTTCAGTGGCAGACCATCGACATGGCGCAGCTCGCTGCT[G/A]
CTTATAGACCACCACCTCCAACTCCACCCCCAACGGCAGCAGACCGGGGCAAGGGAAAGAGGCCAGCAGCAAACACTACTGCCTCAGGGAGTTCTTCCAA
| 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 | 84.30% | 0.10% | 3.47% | 12.12% | NA |
| All Indica | 2759 | 86.20% | 0.20% | 2.72% | 10.84% | NA |
| All Japonica | 1512 | 76.90% | 0.00% | 5.42% | 17.66% | NA |
| Aus | 269 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica I | 595 | 78.50% | 0.00% | 4.03% | 17.48% | NA |
| Indica II | 465 | 85.60% | 0.00% | 4.30% | 10.11% | NA |
| Indica III | 913 | 92.60% | 0.50% | 0.77% | 6.13% | NA |
| Indica Intermediate | 786 | 85.10% | 0.10% | 3.05% | 11.70% | NA |
| Temperate Japonica | 767 | 76.10% | 0.00% | 7.69% | 16.17% | NA |
| Tropical Japonica | 504 | 79.60% | 0.00% | 4.37% | 16.07% | NA |
| Japonica Intermediate | 241 | 73.90% | 0.00% | 0.41% | 25.73% | NA |
| VI/Aromatic | 96 | 94.80% | 0.00% | 5.21% | 0.00% | NA |
| Intermediate | 90 | 90.00% | 0.00% | 2.22% | 7.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1007738693 | C -> T | LOC_Os10g14290.1 | missense_variant ; p.Ala273Thr; MODERATE | nonsynonymous_codon ; A273T | Average:4.415; most accessible tissue: Minghui63 panicle, score: 7.125 | unknown | unknown | DELETERIOUS | 0.04 |
| vg1007738693 | C -> DEL | LOC_Os10g14290.1 | N | frameshift_variant | Average:4.415; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |