| Variant ID: vg0424200268 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 24200268 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TTAACCATACCGGCGTGAGATAGGTCTAGCAGCCGAAGTCGTGGGGCGTGGCCAACCACCAGCGGGTACTCATGCGACGTCCATGGCCAGACGGCTATCG[A/T]
TAGCTCTGCCAGCTTCGGGAGCCACTCCAGCTCGATGGTGTAACAGGCGCAGAACTCGAGATCTATCGTGCTAAAGCTGCTCGTGTCGGATCGTCAGCGT
ACGCTGACGATCCGACACGAGCAGCTTTAGCACGATAGATCTCGAGTTCTGCGCCTGTTACACCATCGAGCTGGAGTGGCTCCCGAAGCTGGCAGAGCTA[T/A]
CGATAGCCGTCTGGCCATGGACGTCGCATGAGTACCCGCTGGTGGTTGGCCACGCCCCACGACTTCGGCTGCTAGACCTATCTCACGCCGGTATGGTTAA
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 98.00% | 0.40% | 0.21% | 1.40% | NA |
| All Indica | 2759 | 97.60% | 0.70% | 0.25% | 1.45% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 89.60% | 0.00% | 1.12% | 9.29% | NA |
| Indica I | 595 | 99.70% | 0.00% | 0.17% | 0.17% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 94.70% | 1.50% | 0.33% | 3.40% | NA |
| Indica Intermediate | 786 | 98.00% | 0.60% | 0.38% | 1.02% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 98.90% | 0.00% | 0.00% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0424200268 | A -> DEL | LOC_Os04g40780.1 | N | frameshift_variant | Average:73.29; most accessible tissue: Zhenshan97 panicle, score: 92.403 | N | N | N | N |
| vg0424200268 | A -> T | LOC_Os04g40780.1 | missense_variant ; p.Ser196Thr; MODERATE | nonsynonymous_codon ; S196T | Average:73.29; most accessible tissue: Zhenshan97 panicle, score: 92.403 | unknown | unknown | TOLERATED | 1.00 |