| Variant ID: vg0915034003 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 15034003 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
TCTGGAAAGGCCAGACGACGGTGCCCCCCACCAATCTGGAAGGCCTCGCTCCGCACCTCAACAGGATGGCCTGGGTTCTCGAACAACTCCCCGAGGAGCT[T/C]
GAGAAGACCATCAAGTCATCCTCGAGGGACCTCGCGCGGGGAGCGGTCGAACTCGTGCTGGCGAGTTACCAGGCCCGGGACCCCAACTTCTCTCCATGGA
TCCATGGAGAGAAGTTGGGGTCCCGGGCCTGGTAACTCGCCAGCACGAGTTCGACCGCTCCCCGCGCGAGGTCCCTCGAGGATGACTTGATGGTCTTCTC[A/G]
AGCTCCTCGGGGAGTTGTTCGAGAACCCAGGCCATCCTGTTGAGGTGCGGAGCGAGGCCTTCCAGATTGGTGGGGGGCACCGTCGTCTGGCCTTTCCAGA
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 11.70% | 0.20% | 4.80% | 83.24% | NA |
| All Indica | 2759 | 0.40% | 0.20% | 1.16% | 98.26% | NA |
| All Japonica | 1512 | 34.70% | 0.10% | 9.79% | 55.49% | NA |
| Aus | 269 | 0.00% | 1.10% | 11.52% | 87.36% | NA |
| Indica I | 595 | 0.20% | 0.00% | 0.67% | 99.16% | NA |
| Indica II | 465 | 1.10% | 0.00% | 0.65% | 98.28% | NA |
| Indica III | 913 | 0.30% | 0.20% | 1.64% | 97.81% | NA |
| Indica Intermediate | 786 | 0.30% | 0.40% | 1.27% | 98.09% | NA |
| Temperate Japonica | 767 | 52.70% | 0.00% | 15.51% | 31.81% | NA |
| Tropical Japonica | 504 | 8.30% | 0.00% | 2.58% | 89.09% | NA |
| Japonica Intermediate | 241 | 32.40% | 0.40% | 6.64% | 60.58% | NA |
| VI/Aromatic | 96 | 9.40% | 0.00% | 6.25% | 84.38% | NA |
| Intermediate | 90 | 12.20% | 1.10% | 11.11% | 75.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0915034003 | T -> DEL | LOC_Os09g25110.1 | N | frameshift_variant | Average:4.47; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0915034003 | T -> C | LOC_Os09g25110.1 | synonymous_variant ; p.Leu872Leu; LOW | synonymous_codon | Average:4.47; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |