| Variant ID: vg0915034284 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 15034284 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
GGCTTCGAGGGCTCGGCCCCTCGGCTCGCGTTCGCCCCCGACTCCGACGAGGAGGGGAACGCCAGCAGTGCAAGCGACGGTGGCAACGAGGCCGGCGACC[T/C]
GGGCGCGTCAGAATGAGCCCCCAGGCCCCCGCCCATCTTAACTTTTTTCTTTTTCTTTCTTCTAAGGCCTTCATGCCTCTTTTTTGTACAAATTAACTTA
TAAGTTAATTTGTACAAAAAAGAGGCATGAAGGCCTTAGAAGAAAGAAAAAGAAAAAAGTTAAGATGGGCGGGGGCCTGGGGGCTCATTCTGACGCGCCC[A/G]
GGTCGCCGGCCTCGTTGCCACCGTCGCTTGCACTGCTGGCGTTCCCCTCCTCGTCGGAGTCGGGGGCGAACGCGAGCCGAGGGGCCGAGCCCTCGAAGCC
| 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 | 18.20% | 0.10% | 11.93% | 69.78% | NA |
| All Indica | 2759 | 3.40% | 0.10% | 16.38% | 80.10% | NA |
| All Japonica | 1512 | 44.20% | 0.00% | 3.64% | 52.12% | NA |
| Aus | 269 | 17.50% | 0.00% | 14.13% | 68.40% | NA |
| Indica I | 595 | 3.40% | 0.00% | 11.09% | 85.55% | NA |
| Indica II | 465 | 3.70% | 0.00% | 11.83% | 84.52% | NA |
| Indica III | 913 | 3.30% | 0.20% | 21.14% | 75.36% | NA |
| Indica Intermediate | 786 | 3.40% | 0.10% | 17.56% | 78.88% | NA |
| Temperate Japonica | 767 | 68.10% | 0.00% | 0.91% | 31.03% | NA |
| Tropical Japonica | 504 | 12.50% | 0.00% | 4.96% | 82.54% | NA |
| Japonica Intermediate | 241 | 34.90% | 0.00% | 9.54% | 55.60% | NA |
| VI/Aromatic | 96 | 20.80% | 2.10% | 10.42% | 66.67% | NA |
| Intermediate | 90 | 32.20% | 0.00% | 10.00% | 57.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0915034284 | T -> DEL | LOC_Os09g25110.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0915034284 | T -> C | LOC_Os09g25110.1 | missense_variant ; p.Leu966Pro; MODERATE | nonsynonymous_codon ; L966P | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | unknown | unknown | TOLERATED | 1.00 |