| Variant ID: vg0424680914 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 24680914 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GAATATATATATACCCCTGGATCTTTACTCCCGGTTTTTGAGAACAACCGGGACTAAAGATATCTTGATATCTTTAGTCCCGGTTGTTGAGAACAACCGG[G/A]
AGTAAAGAAAAGATATTTACTTCCGGTTGTTCTCAACAACCGGGACTAAAGATATCTTTAGTCTCGGTTGTTCTCAACAACCGGGAGTAAATATCTTTTC
GAAAAGATATTTACTCCCGGTTGTTGAGAACAACCGAGACTAAAGATATCTTTAGTCCCGGTTGTTGAGAACAACCGGAAGTAAATATCTTTTCTTTACT[C/T]
CCGGTTGTTCTCAACAACCGGGACTAAAGATATCAAGATATCTTTAGTCCCGGTTGTTCTCAAAAACCGGGAGTAAAGATCCAGGGGTATATATATATTC
| 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 | 26.70% | 0.10% | 13.58% | 59.65% | NA |
| All Indica | 2759 | 7.90% | 0.00% | 5.40% | 86.70% | NA |
| All Japonica | 1512 | 55.60% | 0.30% | 24.14% | 20.04% | NA |
| Aus | 269 | 37.50% | 0.00% | 33.46% | 29.00% | NA |
| Indica I | 595 | 4.50% | 0.00% | 7.73% | 87.73% | NA |
| Indica II | 465 | 6.70% | 0.00% | 4.30% | 89.03% | NA |
| Indica III | 913 | 10.80% | 0.00% | 4.71% | 84.45% | NA |
| Indica Intermediate | 786 | 7.80% | 0.00% | 5.09% | 87.15% | NA |
| Temperate Japonica | 767 | 51.50% | 0.50% | 24.25% | 23.73% | NA |
| Tropical Japonica | 504 | 60.10% | 0.00% | 22.22% | 17.66% | NA |
| Japonica Intermediate | 241 | 58.90% | 0.00% | 27.80% | 13.28% | NA |
| VI/Aromatic | 96 | 80.20% | 0.00% | 15.62% | 4.17% | NA |
| Intermediate | 90 | 27.80% | 0.00% | 25.56% | 46.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0424680914 | G -> DEL | N | N | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0424680914 | 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 |