| Variant ID: vg0424680903 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 24680903 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GGGCGCACCGGGAATATATATATACCCCTGGATCTTTACTCCCGGTTTTTGAGAACAACCGGGACTAAAGATATCTTGATATCTTTAGTCCCGGTTGTTG[A/T]
GAACAACCGGGAGTAAAGAAAAGATATTTACTTCCGGTTGTTCTCAACAACCGGGACTAAAGATATCTTTAGTCTCGGTTGTTCTCAACAACCGGGAGTA
TACTCCCGGTTGTTGAGAACAACCGAGACTAAAGATATCTTTAGTCCCGGTTGTTGAGAACAACCGGAAGTAAATATCTTTTCTTTACTCCCGGTTGTTC[T/A]
CAACAACCGGGACTAAAGATATCAAGATATCTTTAGTCCCGGTTGTTCTCAAAAACCGGGAGTAAAGATCCAGGGGTATATATATATTCCCGGTGCGCCC
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 22.00% | 0.20% | 9.73% | 68.13% | NA |
| All Indica | 2759 | 4.50% | 0.10% | 4.35% | 91.08% | NA |
| All Japonica | 1512 | 51.70% | 0.20% | 15.94% | 32.14% | NA |
| Aus | 269 | 18.20% | 0.00% | 24.54% | 57.25% | NA |
| Indica I | 595 | 3.20% | 0.00% | 1.85% | 94.96% | NA |
| Indica II | 465 | 5.20% | 0.00% | 2.37% | 92.47% | NA |
| Indica III | 913 | 4.30% | 0.10% | 7.45% | 88.17% | NA |
| Indica Intermediate | 786 | 5.20% | 0.30% | 3.82% | 90.71% | NA |
| Temperate Japonica | 767 | 47.80% | 0.30% | 14.21% | 37.68% | NA |
| Tropical Japonica | 504 | 56.00% | 0.20% | 17.86% | 25.99% | NA |
| Japonica Intermediate | 241 | 55.20% | 0.00% | 17.43% | 27.39% | NA |
| VI/Aromatic | 96 | 69.80% | 2.10% | 12.50% | 15.62% | NA |
| Intermediate | 90 | 18.90% | 0.00% | 23.33% | 57.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0424680903 | A -> DEL | N | N | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0424680903 | A -> T | LOC_Os04g41599.1 | intron_variant ; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |