| Variant ID: vg1007738707 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 7738707 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TGAGGCAGTAGTGTTTGCTGCTGGCCTCTTTCCCTTGCCCCGGTCTGCTGCCGTTGGGGGTGGAGTTGGAGGTGGTGGTCTATAAGCAGCAGCGAGCTGC[G/A]
CCATGTCGATGGTCTGCCACTGAACTGCTCCTTGCGGTGCCTGTGGGGCTGCCCCTGCGACGGCGGAGTGGTTTCCGACAACTGTGTGCCCACTGAATAC
GTATTCAGTGGGCACACAGTTGTCGGAAACCACTCCGCCGTCGCAGGGGCAGCCCCACAGGCACCGCAAGGAGCAGTTCAGTGGCAGACCATCGACATGG[C/T]
GCAGCTCGCTGCTGCTTATAGACCACCACCTCCAACTCCACCCCCAACGGCAGCAGACCGGGGCAAGGGAAAGAGGCCAGCAGCAAACACTACTGCCTCA
| 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 | 83.50% | 0.50% | 5.06% | 10.88% | NA |
| All Indica | 2759 | 84.80% | 0.90% | 5.47% | 8.77% | NA |
| All Japonica | 1512 | 77.10% | 0.00% | 5.29% | 17.59% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 78.00% | 0.00% | 5.04% | 16.97% | NA |
| Indica II | 465 | 82.80% | 2.20% | 8.82% | 6.24% | NA |
| Indica III | 913 | 92.20% | 0.40% | 3.61% | 3.72% | NA |
| Indica Intermediate | 786 | 82.70% | 1.40% | 5.98% | 9.92% | NA |
| Temperate Japonica | 767 | 76.30% | 0.00% | 7.43% | 16.30% | NA |
| Tropical Japonica | 504 | 80.20% | 0.00% | 4.17% | 15.67% | NA |
| Japonica Intermediate | 241 | 73.40% | 0.00% | 0.83% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1007738707 | G -> A | LOC_Os10g14290.1 | missense_variant ; p.Ala268Val; MODERATE | nonsynonymous_codon ; A268V | Average:4.415; most accessible tissue: Minghui63 panicle, score: 7.125 | unknown | unknown | TOLERATED | 0.06 |
| vg1007738707 | G -> DEL | LOC_Os10g14290.1 | N | frameshift_variant | Average:4.415; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |