| Variant ID: vg0128509374 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 28509374 |
| Reference Allele: T | Alternative Allele: G |
| Primary Allele: T | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
ACTGAGATCACGGTTTCGTAGGAAGCGGTTCGCGCCGTTTTTCCCACGACACGCTCCTGTCAGGTGCCGTTGTACGGCGGTGCCAGATTGGGGTGTGACA[T/G]
ATATGAACGATGGGAGGCGCGTGATGGTGGCGGTGTCTAGGCCGAACCTGGGCAGCGTCGGCTGCTGCTGCTCCTGCTCCATGACCAGTGGACGATCACG
CGTGATCGTCCACTGGTCATGGAGCAGGAGCAGCAGCAGCCGACGCTGCCCAGGTTCGGCCTAGACACCGCCACCATCACGCGCCTCCCATCGTTCATAT[A/C]
TGTCACACCCCAATCTGGCACCGCCGTACAACGGCACCTGACAGGAGCGTGTCGTGGGAAAAACGGCGCGAACCGCTTCCTACGAAACCGTGATCTCAGT
| 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 | 36.80% | 1.50% | 7.93% | 53.83% | NA |
| All Indica | 2759 | 12.30% | 2.30% | 11.09% | 74.34% | NA |
| All Japonica | 1512 | 88.10% | 0.20% | 3.77% | 7.94% | NA |
| Aus | 269 | 4.10% | 0.40% | 1.86% | 93.68% | NA |
| Indica I | 595 | 5.90% | 2.70% | 3.87% | 87.56% | NA |
| Indica II | 465 | 8.00% | 0.00% | 4.95% | 87.10% | NA |
| Indica III | 913 | 21.90% | 4.30% | 19.82% | 54.00% | NA |
| Indica Intermediate | 786 | 8.50% | 1.00% | 10.05% | 80.41% | NA |
| Temperate Japonica | 767 | 93.00% | 0.40% | 6.13% | 0.52% | NA |
| Tropical Japonica | 504 | 77.00% | 0.00% | 1.79% | 21.23% | NA |
| Japonica Intermediate | 241 | 95.90% | 0.00% | 0.41% | 3.73% | NA |
| VI/Aromatic | 96 | 14.60% | 0.00% | 2.08% | 83.33% | NA |
| Intermediate | 90 | 46.70% | 2.20% | 5.56% | 45.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0128509374 | T -> G | LOC_Os01g49570.1 | missense_variant ; p.Tyr67Ser; MODERATE | nonsynonymous_codon ; Y67S | Average:21.498; most accessible tissue: Zhenshan97 panicle, score: 39.652 | unknown | unknown | TOLERATED | 0.55 |
| vg0128509374 | T -> DEL | LOC_Os01g49570.1 | N | frameshift_variant | Average:21.498; most accessible tissue: Zhenshan97 panicle, score: 39.652 | N | N | N | N |