| Variant ID: vg0430653203 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 30653203 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
AGCCGTATGGAGCCCGGCCGGGGGACACCGATCACTCGATACGGACCCTCCCACATTGGTGAGAGCTTGCTCAATCCAGCACGCGTTTAGACGCGGCGTA[A/G]
GACGAGGTCGTCGACGCAGAGTGATCGGGCCCGGACGTGGCGCTGATGGTAGCGCCGCAGGCTCTGCTGGTAGCGCGCGGCTCGGAGGGCCGCGCGCCTC
GAGGCGCGCGGCCCTCCGAGCCGCGCGCTACCAGCAGAGCCTGCGGCGCTACCATCAGCGCCACGTCCGGGCCCGATCACTCTGCGTCGACGACCTCGTC[T/C]
TACGCCGCGTCTAAACGCGTGCTGGATTGAGCAAGCTCTCACCAATGTGGGAGGGTCCGTATCGAGTGATCGGTGTCCCCCGGCCGGGCTCCATACGGCT
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 13.60% | 0.10% | 27.66% | 58.63% | NA |
| All Indica | 2759 | 2.00% | 0.00% | 35.67% | 62.38% | NA |
| All Japonica | 1512 | 37.40% | 0.30% | 10.05% | 52.18% | NA |
| Aus | 269 | 1.10% | 0.00% | 44.98% | 53.90% | NA |
| Indica I | 595 | 1.00% | 0.00% | 18.49% | 80.50% | NA |
| Indica II | 465 | 3.20% | 0.00% | 32.26% | 64.52% | NA |
| Indica III | 913 | 1.80% | 0.00% | 53.56% | 44.69% | NA |
| Indica Intermediate | 786 | 2.20% | 0.00% | 29.90% | 67.94% | NA |
| Temperate Japonica | 767 | 63.00% | 0.00% | 0.39% | 36.64% | NA |
| Tropical Japonica | 504 | 6.30% | 1.00% | 21.03% | 71.63% | NA |
| Japonica Intermediate | 241 | 21.20% | 0.00% | 17.84% | 61.00% | NA |
| VI/Aromatic | 96 | 3.10% | 0.00% | 26.04% | 70.83% | NA |
| Intermediate | 90 | 17.80% | 1.10% | 27.78% | 53.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0430653203 | A -> DEL | LOC_Os04g51730.1 | N | frameshift_variant | Average:8.608; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |
| vg0430653203 | A -> G | LOC_Os04g51730.1 | synonymous_variant ; p.Leu387Leu; LOW | synonymous_codon | Average:8.608; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |