| Variant ID: vg0131447782 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 31447782 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
CGGTGTAGTCGATGCACATCCGAAGCTTGCCGTTCGCCTTGGGAACGACCACCGGGTTCGCCAGCCACTCCGGATGGATGACCTCACGGATGAATCCGGC[T/C]
TCCAGAAGTCGCGCCACCTCCTCGCGGATGAAGGCTTGACGTTCCGGGGCCTGCCGCCGCACTTTCTGCCGGACCGGCCTTGCGCCCGGCCGCACGGCGA
TCGCCGTGCGGCCGGGCGCAAGGCCGGTCCGGCAGAAAGTGCGGCGGCAGGCCCCGGAACGTCAAGCCTTCATCCGCGAGGAGGTGGCGCGACTTCTGGA[A/G]
GCCGGATTCATCCGTGAGGTCATCCATCCGGAGTGGCTGGCGAACCCGGTGGTCGTTCCCAAGGCGAACGGCAAGCTTCGGATGTGCATCGACTACACCG
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 31.10% | 0.10% | 0.53% | 68.30% | NA |
| All Indica | 2759 | 2.20% | 0.20% | 0.47% | 97.10% | NA |
| All Japonica | 1512 | 82.60% | 0.00% | 0.73% | 16.67% | NA |
| Aus | 269 | 1.10% | 0.00% | 0.00% | 98.88% | NA |
| Indica I | 595 | 3.20% | 0.30% | 1.18% | 95.29% | NA |
| Indica II | 465 | 0.60% | 0.00% | 0.00% | 99.35% | NA |
| Indica III | 913 | 0.80% | 0.00% | 0.11% | 99.12% | NA |
| Indica Intermediate | 786 | 4.20% | 0.40% | 0.64% | 94.78% | NA |
| Temperate Japonica | 767 | 86.60% | 0.00% | 0.91% | 12.52% | NA |
| Tropical Japonica | 504 | 90.30% | 0.00% | 0.00% | 9.72% | NA |
| Japonica Intermediate | 241 | 53.90% | 0.00% | 1.66% | 44.40% | NA |
| VI/Aromatic | 96 | 96.90% | 0.00% | 0.00% | 3.12% | NA |
| Intermediate | 90 | 67.80% | 0.00% | 1.11% | 31.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0131447782 | T -> DEL | LOC_Os01g54660.1 | N | frameshift_variant | Average:18.469; most accessible tissue: Zhenshan97 panicle, score: 39.652 | N | N | N | N |
| vg0131447782 | T -> C | LOC_Os01g54660.1 | synonymous_variant ; p.Glu851Glu; LOW | synonymous_codon | Average:18.469; most accessible tissue: Zhenshan97 panicle, score: 39.652 | N | N | N | N |