| Variant ID: vg0131450153 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 31450153 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TCCAGCCAACGTTGGGCTGGAGACTCCGGGTCATGGGCGACGGGCGGGTGACGTAGGAGCGCGCCCGCAGCTTGGAGCGCGCCCTGGGGCGTGCTGCCGT[T/C]
GCCGTAGACGAGGAGGCGACGCTCCTCATCTCGCCGCCCTTCTCCACCTCCTGTGGATGTCGAAGTCGCGGATCCTTCGGCCCTCTCAAGTGCCTTCTCC
GGAGAAGGCACTTGAGAGGGCCGAAGGATCCGCGACTTCGACATCCACAGGAGGTGGAGAAGGGCGGCGAGATGAGGAGCGTCGCCTCCTCGTCTACGGC[A/G]
ACGGCAGCACGCCCCAGGGCGCGCTCCAAGCTGCGGGCGCGCTCCTACGTCACCCGCCCGTCGCCCATGACCCGGAGTCTCCAGCCCAACGTTGGCTGGA
| 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 | 16.20% | 14.60% | 4.21% | 64.96% | NA |
| All Indica | 2759 | 0.50% | 1.90% | 6.13% | 91.45% | NA |
| All Japonica | 1512 | 41.30% | 40.50% | 1.46% | 16.80% | NA |
| Aus | 269 | 0.70% | 0.00% | 1.12% | 98.14% | NA |
| Indica I | 595 | 0.00% | 3.00% | 7.73% | 89.24% | NA |
| Indica II | 465 | 0.40% | 0.90% | 7.10% | 91.61% | NA |
| Indica III | 913 | 0.40% | 0.20% | 3.50% | 95.84% | NA |
| Indica Intermediate | 786 | 1.00% | 3.70% | 7.38% | 87.91% | NA |
| Temperate Japonica | 767 | 20.10% | 66.00% | 1.69% | 12.26% | NA |
| Tropical Japonica | 504 | 83.90% | 5.00% | 1.39% | 9.72% | NA |
| Japonica Intermediate | 241 | 19.50% | 33.60% | 0.83% | 46.06% | NA |
| VI/Aromatic | 96 | 91.70% | 2.10% | 2.08% | 4.17% | NA |
| Intermediate | 90 | 41.10% | 27.80% | 3.33% | 27.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0131450153 | T -> DEL | LOC_Os01g54660.1 | N | frameshift_variant | Average:34.543; most accessible tissue: Zhenshan97 panicle, score: 75.67 | N | N | N | N |
| vg0131450153 | T -> C | LOC_Os01g54660.1 | missense_variant ; p.Asn74Asp; MODERATE | nonsynonymous_codon | Average:34.543; most accessible tissue: Zhenshan97 panicle, score: 75.67 | unknown | unknown | TOLERATED | 1.00 |