| Variant ID: vg1007738749 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 7738749 |
| Reference Allele: T | Alternative Allele: G,C |
| Primary Allele: T | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
GTCTGCTGCCGTTGGGGGTGGAGTTGGAGGTGGTGGTCTATAAGCAGCAGCGAGCTGCGCCATGTCGATGGTCTGCCACTGAACTGCTCCTTGCGGTGCC[T/G,C]
GTGGGGCTGCCCCTGCGACGGCGGAGTGGTTTCCGACAACTGTGTGCCCACTGAATACCGCGTGGTGAAGGTCAATGTGCTTCAGAGGATCATTCCTGAA
TTCAGGAATGATCCTCTGAAGCACATTGACCTTCACCACGCGGTATTCAGTGGGCACACAGTTGTCGGAAACCACTCCGCCGTCGCAGGGGCAGCCCCAC[A/C,G]
GGCACCGCAAGGAGCAGTTCAGTGGCAGACCATCGACATGGCGCAGCTCGCTGCTGCTTATAGACCACCACCTCCAACTCCACCCCCAACGGCAGCAGAC
| Populations | Population Size | Frequency of T(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 69.30% | 2.50% | 14.58% | 13.46% | C: 0.11% |
| All Indica | 2759 | 69.00% | 3.30% | 14.53% | 12.98% | C: 0.18% |
| All Japonica | 1512 | 68.10% | 0.60% | 13.49% | 17.79% | NA |
| Aus | 269 | 66.50% | 5.90% | 27.51% | 0.00% | NA |
| Indica I | 595 | 62.50% | 0.30% | 18.66% | 18.49% | NA |
| Indica II | 465 | 66.70% | 1.30% | 17.63% | 14.41% | NA |
| Indica III | 913 | 74.00% | 6.90% | 11.72% | 6.90% | C: 0.44% |
| Indica Intermediate | 786 | 69.60% | 2.40% | 12.85% | 15.01% | C: 0.13% |
| Temperate Japonica | 767 | 63.10% | 0.80% | 19.95% | 16.17% | NA |
| Tropical Japonica | 504 | 73.40% | 0.60% | 9.52% | 16.47% | NA |
| Japonica Intermediate | 241 | 73.00% | 0.00% | 1.24% | 25.73% | NA |
| VI/Aromatic | 96 | 92.70% | 2.10% | 5.21% | 0.00% | NA |
| Intermediate | 90 | 82.20% | 2.20% | 5.56% | 10.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1007738749 | T -> C | LOC_Os10g14290.1 | missense_variant ; p.Gln254Arg; MODERATE | nonsynonymous_codon ; Q254R | Average:4.415; most accessible tissue: Minghui63 panicle, score: 7.125 | unknown | unknown | TOLERATED | 0.31 |
| vg1007738749 | T -> G | LOC_Os10g14290.1 | missense_variant ; p.Gln254Pro; MODERATE | nonsynonymous_codon ; Q254P | Average:4.415; most accessible tissue: Minghui63 panicle, score: 7.125 | unknown | unknown | TOLERATED | 0.27 |
| vg1007738749 | T -> DEL | LOC_Os10g14290.1 | N | frameshift_variant | Average:4.415; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |