| Variant ID: vg0424680902 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 24680902 |
| Reference Allele: G | Alternative Allele: T,C |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
AGGGCGCACCGGGAATATATATATACCCCTGGATCTTTACTCCCGGTTTTTGAGAACAACCGGGACTAAAGATATCTTGATATCTTTAGTCCCGGTTGTT[G/T,C]
AGAACAACCGGGAGTAAAGAAAAGATATTTACTTCCGGTTGTTCTCAACAACCGGGACTAAAGATATCTTTAGTCTCGGTTGTTCTCAACAACCGGGAGT
ACTCCCGGTTGTTGAGAACAACCGAGACTAAAGATATCTTTAGTCCCGGTTGTTGAGAACAACCGGAAGTAAATATCTTTTCTTTACTCCCGGTTGTTCT[C/A,G]
AACAACCGGGACTAAAGATATCAAGATATCTTTAGTCCCGGTTGTTCTCAAAAACCGGGAGTAAAGATCCAGGGGTATATATATATTCCCGGTGCGCCCT
| Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 21.70% | 0.20% | 9.84% | 68.13% | T: 0.13% |
| All Indica | 2759 | 4.50% | 0.10% | 4.35% | 91.08% | NA |
| All Japonica | 1512 | 51.10% | 0.20% | 16.27% | 32.14% | T: 0.33% |
| Aus | 269 | 18.20% | 0.00% | 24.54% | 57.25% | NA |
| Indica I | 595 | 3.20% | 0.00% | 2.02% | 94.79% | NA |
| Indica II | 465 | 5.20% | 0.00% | 2.37% | 92.47% | NA |
| Indica III | 913 | 4.30% | 0.10% | 7.34% | 88.28% | NA |
| Indica Intermediate | 786 | 5.20% | 0.30% | 3.82% | 90.71% | NA |
| Temperate Japonica | 767 | 46.70% | 0.30% | 14.86% | 37.68% | T: 0.52% |
| Tropical Japonica | 504 | 56.00% | 0.20% | 17.86% | 25.99% | NA |
| Japonica Intermediate | 241 | 54.80% | 0.00% | 17.43% | 27.39% | T: 0.41% |
| VI/Aromatic | 96 | 68.80% | 2.10% | 12.50% | 15.62% | T: 1.04% |
| 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0424680902 | G -> C | LOC_Os04g41599.1 | intron_variant ; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0424680902 | G -> DEL | N | N | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0424680902 | G -> T | LOC_Os04g41599.1 | intron_variant ; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |