| Variant ID: vg1007913125 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 7913125 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TAACTATTTACGCTTCCGCTTGTTATACTCTGAATTGTATCAACTTTTGGTGTACCTTGCCTCCTGGGACAAGGATTAATGCACGCACGTAAGGAACGCC[C/T]
GTTGGGTTATTTCCGGTCGTGACAGTGGAGCTGAAGCCATCGCTTGATCTTTTCTTTTGTAAGTGTGTAACGTTATTATTACGATGGATTTGTATATTAA
TTAATATACAAATCCATCGTAATAATAACGTTACACACTTACAAAAGAAAAGATCAAGCGATGGCTTCAGCTCCACTGTCACGACCGGAAATAACCCAAC[G/A]
GGCGTTCCTTACGTGCGTGCATTAATCCTTGTCCCAGGAGGCAAGGTACACCAAAAGTTGATACAATTCAGAGTATAACAAGCGGAAGCGTAAATAGTTA
| 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 | 14.50% | 1.20% | 35.40% | 48.90% | NA |
| All Indica | 2759 | 3.90% | 0.00% | 36.21% | 59.88% | NA |
| All Japonica | 1512 | 36.60% | 3.60% | 26.72% | 33.00% | NA |
| Aus | 269 | 2.20% | 0.00% | 58.74% | 39.03% | NA |
| Indica I | 595 | 5.50% | 0.00% | 25.04% | 69.41% | NA |
| Indica II | 465 | 6.70% | 0.00% | 32.69% | 60.65% | NA |
| Indica III | 913 | 1.50% | 0.00% | 46.99% | 51.48% | NA |
| Indica Intermediate | 786 | 3.70% | 0.10% | 34.22% | 61.96% | NA |
| Temperate Japonica | 767 | 56.10% | 0.40% | 18.12% | 25.42% | NA |
| Tropical Japonica | 504 | 5.60% | 3.40% | 47.22% | 43.85% | NA |
| Japonica Intermediate | 241 | 39.80% | 14.50% | 11.20% | 34.44% | NA |
| VI/Aromatic | 96 | 2.10% | 0.00% | 73.96% | 23.96% | NA |
| Intermediate | 90 | 17.80% | 1.10% | 45.56% | 35.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1007913125 | C -> T | LOC_Os10g15100.1 | intron_variant ; MODIFIER | silent_mutation | Average:8.455; most accessible tissue: Minghui63 panicle, score: 25.313 | N | N | N | N |
| vg1007913125 | C -> DEL | N | N | silent_mutation | Average:8.455; most accessible tissue: Minghui63 panicle, score: 25.313 | N | N | N | N |