| Variant ID: vg0908137198 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 8137198 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
GCGTGTGTTTTTCTAAGCTCTCGCATTCTTTCGTGTGCGCCAAGCTTTTCCTGTTCAGCCCAATGGCCGAACAAGCAAAGGCGCACAACCTCTCTCCGAG[T/C]
GTTAGCGGTGACGACGGGGAGCCGAACCCACGCCGTCGAGCTCGTACTCCACCGCCCCCTCCACGCCAAAGTCCTAGGCGGGAGGAGGCGCTCGAGAGGG
CCCTCTCGAGCGCCTCCTCCCGCCTAGGACTTTGGCGTGGAGGGGGCGGTGGAGTACGAGCTCGACGGCGTGGGTTCGGCTCCCCGTCGTCACCGCTAAC[A/G]
CTCGGAGAGAGGTTGTGCGCCTTTGCTTGTTCGGCCATTGGGCTGAACAGGAAAAGCTTGGCGCACACGAAAGAATGCGAGAGCTTAGAAAAACACACGC
| 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 | 48.50% | 0.70% | 8.00% | 42.78% | NA |
| All Indica | 2759 | 33.50% | 0.10% | 4.20% | 62.27% | NA |
| All Japonica | 1512 | 79.20% | 1.10% | 14.35% | 5.36% | NA |
| Aus | 269 | 7.10% | 5.60% | 11.52% | 75.84% | NA |
| Indica I | 595 | 12.30% | 0.00% | 0.84% | 86.89% | NA |
| Indica II | 465 | 65.20% | 0.00% | 2.15% | 32.69% | NA |
| Indica III | 913 | 30.30% | 0.10% | 7.23% | 62.32% | NA |
| Indica Intermediate | 786 | 34.40% | 0.10% | 4.45% | 61.07% | NA |
| Temperate Japonica | 767 | 90.50% | 0.40% | 8.08% | 1.04% | NA |
| Tropical Japonica | 504 | 72.00% | 2.20% | 18.25% | 7.54% | NA |
| Japonica Intermediate | 241 | 58.50% | 0.80% | 26.14% | 14.52% | NA |
| VI/Aromatic | 96 | 91.70% | 1.00% | 4.17% | 3.12% | NA |
| Intermediate | 90 | 71.10% | 0.00% | 11.11% | 17.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0908137198 | T -> DEL | LOC_Os09g13850.1 | N | frameshift_variant | Average:19.879; most accessible tissue: Minghui63 panicle, score: 46.754 | N | N | N | N |
| vg0908137198 | T -> C | LOC_Os09g13850.1 | synonymous_variant ; p.Ser13Ser; LOW | synonymous_codon | Average:19.879; most accessible tissue: Minghui63 panicle, score: 46.754 | N | N | N | N |