| Variant ID: vg0221509541 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 21509541 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CCGGGATCGAGGCCGCCGGGGGTGACGACAGGGTCATGGCGAATTTCTTTCCCATGGCCCTGAAGGGACAGGCACGGGGTTGGCTAATGAACTTGCCACC[C/T]
GCGTCCGTCCACTCTTGGGAGGATTTGTGCCAACAGTTCACCATGAACTTTCAAGGCACATATCCGTGCCCAGGTGAAGAAGCGGACCTGCACGCAGTAC
GTACTGCGTGCAGGTCCGCTTCTTCACCTGGGCACGGATATGTGCCTTGAAAGTTCATGGTGAACTGTTGGCACAAATCCTCCCAAGAGTGGACGGACGC[G/A]
GGTGGCAAGTTCATTAGCCAACCCCGTGCCTGTCCCTTCAGGGCCATGGGAAAGAAATTCGCCATGACCCTGTCGTCACCCCCGGCGGCCTCGATCCCGG
| 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 | 34.80% | 0.50% | 0.49% | 64.16% | NA |
| All Indica | 2759 | 2.50% | 0.00% | 0.72% | 96.74% | NA |
| All Japonica | 1512 | 95.00% | 1.50% | 0.07% | 3.44% | NA |
| Aus | 269 | 0.40% | 0.00% | 0.00% | 99.63% | NA |
| Indica I | 595 | 2.50% | 0.00% | 0.17% | 97.31% | NA |
| Indica II | 465 | 3.20% | 0.00% | 0.65% | 96.13% | NA |
| Indica III | 913 | 1.50% | 0.00% | 0.77% | 97.70% | NA |
| Indica Intermediate | 786 | 3.30% | 0.00% | 1.15% | 95.55% | NA |
| Temperate Japonica | 767 | 98.40% | 0.10% | 0.13% | 1.30% | NA |
| Tropical Japonica | 504 | 89.70% | 3.40% | 0.00% | 6.94% | NA |
| Japonica Intermediate | 241 | 95.00% | 2.10% | 0.00% | 2.90% | NA |
| VI/Aromatic | 96 | 91.70% | 0.00% | 1.04% | 7.29% | NA |
| Intermediate | 90 | 57.80% | 1.10% | 1.11% | 40.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0221509541 | C -> T | LOC_Os02g35800.1 | synonymous_variant ; p.Pro293Pro; LOW | synonymous_codon | Average:4.787; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0221509541 | C -> DEL | LOC_Os02g35800.1 | N | frameshift_variant | Average:4.787; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |