| Variant ID: vg0908137189 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 8137189 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GGGGGCTCTGCGTGTGTTTTTCTAAGCTCTCGCATTCTTTCGTGTGCGCCAAGCTTTTCCTGTTCAGCCCAATGGCCGAACAAGCAAAGGCGCACAACCT[C/T]
TCTCCGAGTGTTAGCGGTGACGACGGGGAGCCGAACCCACGCCGTCGAGCTCGTACTCCACCGCCCCCTCCACGCCAAAGTCCTAGGCGGGAGGAGGCGC
GCGCCTCCTCCCGCCTAGGACTTTGGCGTGGAGGGGGCGGTGGAGTACGAGCTCGACGGCGTGGGTTCGGCTCCCCGTCGTCACCGCTAACACTCGGAGA[G/A]
AGGTTGTGCGCCTTTGCTTGTTCGGCCATTGGGCTGAACAGGAAAAGCTTGGCGCACACGAAAGAATGCGAGAGCTTAGAAAAACACACGCAGAGCCCCC
| 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 | 48.50% | 0.70% | 6.47% | 44.33% | NA |
| All Indica | 2759 | 33.40% | 0.10% | 1.52% | 64.99% | NA |
| All Japonica | 1512 | 79.20% | 1.00% | 14.55% | 5.22% | NA |
| Aus | 269 | 7.40% | 5.20% | 11.52% | 75.84% | NA |
| Indica I | 595 | 12.10% | 0.00% | 1.01% | 86.89% | NA |
| Indica II | 465 | 64.90% | 0.00% | 1.08% | 33.98% | NA |
| Indica III | 913 | 30.40% | 0.10% | 1.42% | 68.02% | NA |
| Indica Intermediate | 786 | 34.40% | 0.10% | 2.29% | 63.23% | NA |
| Temperate Japonica | 767 | 90.20% | 0.40% | 8.34% | 1.04% | NA |
| Tropical Japonica | 504 | 72.40% | 2.00% | 18.45% | 7.14% | NA |
| Japonica Intermediate | 241 | 58.50% | 0.80% | 26.14% | 14.52% | NA |
| VI/Aromatic | 96 | 92.70% | 1.00% | 4.17% | 2.08% | NA |
| Intermediate | 90 | 71.10% | 0.00% | 10.00% | 18.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0908137189 | C -> DEL | LOC_Os09g13850.1 | N | frameshift_variant | Average:19.415; most accessible tissue: Minghui63 panicle, score: 46.754 | N | N | N | N |
| vg0908137189 | C -> T | LOC_Os09g13850.1 | synonymous_variant ; p.Leu10Leu; LOW | synonymous_codon | Average:19.415; most accessible tissue: Minghui63 panicle, score: 46.754 | N | N | N | N |