| Variant ID: vg0424680896 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 24680896 |
| Reference Allele: G | Alternative Allele: A,T |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
AAGACGAGGGCGCACCGGGAATATATATATACCCCTGGATCTTTACTCCCGGTTTTTGAGAACAACCGGGACTAAAGATATCTTGATATCTTTAGTCCCG[G/A,T]
TTGTTGAGAACAACCGGGAGTAAAGAAAAGATATTTACTTCCGGTTGTTCTCAACAACCGGGACTAAAGATATCTTTAGTCTCGGTTGTTCTCAACAACC
GGTTGTTGAGAACAACCGAGACTAAAGATATCTTTAGTCCCGGTTGTTGAGAACAACCGGAAGTAAATATCTTTTCTTTACTCCCGGTTGTTCTCAACAA[C/T,A]
CGGGACTAAAGATATCAAGATATCTTTAGTCCCGGTTGTTCTCAAAAACCGGGAGTAAAGATCCAGGGGTATATATATATTCCCGGTGCGCCCTCGTCTT
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 24.10% | 0.10% | 11.40% | 64.33% | T: 0.06% |
| All Indica | 2759 | 7.10% | 0.00% | 6.34% | 86.52% | NA |
| All Japonica | 1512 | 50.80% | 0.20% | 19.11% | 29.70% | T: 0.20% |
| Aus | 269 | 30.10% | 0.00% | 14.13% | 55.76% | NA |
| Indica I | 595 | 2.70% | 0.00% | 10.76% | 86.55% | NA |
| Indica II | 465 | 6.50% | 0.00% | 4.95% | 88.60% | NA |
| Indica III | 913 | 10.40% | 0.00% | 4.82% | 84.78% | NA |
| Indica Intermediate | 786 | 7.00% | 0.10% | 5.60% | 87.28% | NA |
| Temperate Japonica | 767 | 45.20% | 0.40% | 19.56% | 34.81% | NA |
| Tropical Japonica | 504 | 56.90% | 0.00% | 18.65% | 23.81% | T: 0.60% |
| Japonica Intermediate | 241 | 55.60% | 0.00% | 18.67% | 25.73% | NA |
| VI/Aromatic | 96 | 77.10% | 0.00% | 13.54% | 9.38% | NA |
| Intermediate | 90 | 23.30% | 0.00% | 26.67% | 50.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0424680896 | G -> DEL | N | N | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0424680896 | G -> A | LOC_Os04g41599.1 | intron_variant ; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0424680896 | 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 |