| Variant ID: vg1007738723 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 7738723 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GCTGCTGGCCTCTTTCCCTTGCCCCGGTCTGCTGCCGTTGGGGGTGGAGTTGGAGGTGGTGGTCTATAAGCAGCAGCGAGCTGCGCCATGTCGATGGTCT[G/A]
CCACTGAACTGCTCCTTGCGGTGCCTGTGGGGCTGCCCCTGCGACGGCGGAGTGGTTTCCGACAACTGTGTGCCCACTGAATACCGCGTGGTGAAGGTCA
TGACCTTCACCACGCGGTATTCAGTGGGCACACAGTTGTCGGAAACCACTCCGCCGTCGCAGGGGCAGCCCCACAGGCACCGCAAGGAGCAGTTCAGTGG[C/T]
AGACCATCGACATGGCGCAGCTCGCTGCTGCTTATAGACCACCACCTCCAACTCCACCCCCAACGGCAGCAGACCGGGGCAAGGGAAAGAGGCCAGCAGC
| 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 | 84.40% | 0.10% | 4.97% | 10.52% | NA |
| All Indica | 2759 | 87.40% | 0.00% | 4.42% | 8.19% | NA |
| All Japonica | 1512 | 75.40% | 0.10% | 6.94% | 17.53% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 78.50% | 0.00% | 4.54% | 16.97% | NA |
| Indica II | 465 | 87.70% | 0.00% | 6.24% | 6.02% | NA |
| Indica III | 913 | 93.90% | 0.00% | 3.29% | 2.85% | NA |
| Indica Intermediate | 786 | 86.30% | 0.10% | 4.58% | 9.03% | NA |
| Temperate Japonica | 767 | 72.60% | 0.30% | 10.95% | 16.17% | NA |
| Tropical Japonica | 504 | 80.40% | 0.00% | 3.97% | 15.67% | NA |
| Japonica Intermediate | 241 | 73.90% | 0.00% | 0.41% | 25.73% | NA |
| VI/Aromatic | 96 | 94.80% | 0.00% | 5.21% | 0.00% | NA |
| Intermediate | 90 | 90.00% | 0.00% | 3.33% | 6.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1007738723 | G -> A | LOC_Os10g14290.1 | stop_gained ; p.Gln263*; HIGH | stop_gained | Average:4.415; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1007738723 | G -> DEL | LOC_Os10g14290.1 | N | frameshift_variant | Average:4.415; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |