| Variant ID: vg1007738762 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 7738762 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GGGGGTGGAGTTGGAGGTGGTGGTCTATAAGCAGCAGCGAGCTGCGCCATGTCGATGGTCTGCCACTGAACTGCTCCTTGCGGTGCCTGTGGGGCTGCCC[C/T]
TGCGACGGCGGAGTGGTTTCCGACAACTGTGTGCCCACTGAATACCGCGTGGTGAAGGTCAATGTGCTTCAGAGGATCATTCCTGAAGCTTAAGACACCT
AGGTGTCTTAAGCTTCAGGAATGATCCTCTGAAGCACATTGACCTTCACCACGCGGTATTCAGTGGGCACACAGTTGTCGGAAACCACTCCGCCGTCGCA[G/A]
GGGCAGCCCCACAGGCACCGCAAGGAGCAGTTCAGTGGCAGACCATCGACATGGCGCAGCTCGCTGCTGCTTATAGACCACCACCTCCAACTCCACCCCC
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 78.70% | 0.30% | 6.14% | 14.88% | NA |
| All Indica | 2759 | 79.20% | 0.30% | 5.87% | 14.64% | NA |
| All Japonica | 1512 | 72.90% | 0.40% | 7.47% | 19.18% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 76.60% | 0.00% | 4.71% | 18.66% | NA |
| Indica II | 465 | 72.90% | 1.10% | 8.82% | 17.20% | NA |
| Indica III | 913 | 85.00% | 0.10% | 6.13% | 8.76% | NA |
| Indica Intermediate | 786 | 78.20% | 0.10% | 4.71% | 16.92% | NA |
| Temperate Japonica | 767 | 80.30% | 0.00% | 1.56% | 18.12% | NA |
| Tropical Japonica | 504 | 61.50% | 1.00% | 19.84% | 17.66% | NA |
| Japonica Intermediate | 241 | 73.40% | 0.40% | 0.41% | 25.73% | NA |
| VI/Aromatic | 96 | 90.60% | 1.00% | 8.33% | 0.00% | NA |
| Intermediate | 90 | 82.20% | 0.00% | 7.78% | 10.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1007738762 | C -> T | LOC_Os10g14290.1 | missense_variant ; p.Gly250Arg; MODERATE | nonsynonymous_codon ; G250R | Average:4.415; most accessible tissue: Minghui63 panicle, score: 7.125 | unknown | unknown | DELETERIOUS | 0.00 |
| vg1007738762 | C -> DEL | LOC_Os10g14290.1 | N | frameshift_variant | Average:4.415; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |