| Variant ID: vg0700388280 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 388280 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TCCAGCCACGGGGGCCGGTGTTGAACCGCTACATCCCCTGCGTCCTCCGCAAGAAGTGGGACGACTGGAAGAGCGACTGGTTCTACACCCCCCTCGCCGA[C/T]
GAAGCGCGCCTCCGACTTCCGAGCCAGCCCCCGGCGCAGGTCTCCAGCTGGCGGGCGCCGGTAGATCTGGGGGAGGAGTACGACGCCGTCCTCGACCGCC
GGCGGTCGAGGACGGCGTCGTACTCCTCCCCCAGATCTACCGGCGCCCGCCAGCTGGAGACCTGCGCCGGGGGCTGGCTCGGAAGTCGGAGGCGCGCTTC[G/A]
TCGGCGAGGGGGGTGTAGAACCAGTCGCTCTTCCAGTCGTCCCACTTCTTGCGGAGGACGCAGGGGATGTAGCGGTTCAACACCGGCCCCCGTGGCTGGA
| 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 | 41.80% | 0.20% | 1.44% | 56.62% | NA |
| All Indica | 2759 | 15.50% | 0.00% | 2.21% | 82.24% | NA |
| All Japonica | 1512 | 92.30% | 0.50% | 0.26% | 6.94% | NA |
| Aus | 269 | 1.90% | 0.00% | 0.00% | 98.14% | NA |
| Indica I | 595 | 5.50% | 0.00% | 3.03% | 91.43% | NA |
| Indica II | 465 | 56.60% | 0.00% | 1.94% | 41.51% | NA |
| Indica III | 913 | 1.40% | 0.00% | 2.08% | 96.50% | NA |
| Indica Intermediate | 786 | 15.30% | 0.00% | 1.91% | 82.82% | NA |
| Temperate Japonica | 767 | 96.70% | 0.00% | 0.39% | 2.87% | NA |
| Tropical Japonica | 504 | 84.50% | 0.20% | 0.00% | 15.28% | NA |
| Japonica Intermediate | 241 | 94.20% | 2.90% | 0.41% | 2.49% | NA |
| VI/Aromatic | 96 | 88.50% | 0.00% | 1.04% | 10.42% | NA |
| Intermediate | 90 | 66.70% | 0.00% | 2.22% | 31.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0700388280 | C -> DEL | LOC_Os07g01640.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0700388280 | C -> T | LOC_Os07g01640.1 | synonymous_variant ; p.Asp107Asp; LOW | synonymous_codon | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |