| Variant ID: vg0300824115 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 824115 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GGTCGGAGGTTGCCCTCACCTTCGACCAGACCGACCACCCACCGTGCGTTGCCCGGGGAGGGCAGATTGCGATGGTGGTTTCTCCCACCGTTTGCAACGT[G/A]
AAGTTGGGGCGTATCCTCATTGATGGGGGAGCGGCCCTCAACATCCTTTCCCCTGCGGCCTTTGACGCCATCAAGGCCCCGGGGATGGTGCTCCGGCCGT
ACGGCCGGAGCACCATCCCCGGGGCCTTGATGGCGTCAAAGGCCGCAGGGGAAAGGATGTTGAGGGCCGCTCCCCCATCAATGAGGATACGCCCCAACTT[C/T]
ACGTTGCAAACGGTGGGAGAAACCACCATCGCAATCTGCCCTCCCCGGGCAACGCACGGTGGGTGGTCGGTCTGGTCGAAGGTGAGGGCAACCTCCGACC
| 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 | 13.10% | 0.10% | 0.49% | 86.35% | NA |
| All Indica | 2759 | 1.20% | 0.00% | 0.04% | 98.73% | NA |
| All Japonica | 1512 | 37.10% | 0.00% | 0.07% | 62.83% | NA |
| Aus | 269 | 1.50% | 1.10% | 1.49% | 95.91% | NA |
| Indica I | 595 | 0.20% | 0.00% | 0.00% | 99.83% | NA |
| Indica II | 465 | 4.50% | 0.00% | 0.00% | 95.48% | NA |
| Indica III | 913 | 0.40% | 0.10% | 0.11% | 99.34% | NA |
| Indica Intermediate | 786 | 0.90% | 0.00% | 0.00% | 99.11% | NA |
| Temperate Japonica | 767 | 60.80% | 0.00% | 0.00% | 39.24% | NA |
| Tropical Japonica | 504 | 6.30% | 0.00% | 0.00% | 93.65% | NA |
| Japonica Intermediate | 241 | 26.10% | 0.00% | 0.41% | 73.44% | NA |
| VI/Aromatic | 96 | 4.20% | 1.00% | 16.67% | 78.12% | NA |
| Intermediate | 90 | 16.70% | 0.00% | 1.11% | 82.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0300824115 | G -> A | LOC_Os03g02350.1 | synonymous_variant ; p.Val622Val; LOW | synonymous_codon | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0300824115 | G -> DEL | LOC_Os03g02350.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |