| Variant ID: vg0725420600 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 25420600 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GGCACAAATCTTCCCAGGAGTGGACCGACGCGGGTGGCAGGTTCATTAGCCAACCCCGCGCCTGTCCTTTTAGGGCCATGGGAAAGAAGTTCGCCATGAC[C/T]
CTGTCGTCACCCCCAGCGGCCTCGATCCCGGTCGTATAGACCTGGAGAAACTCGGTGGGGTTGACGCTCCCATCGTACTTCTCGGTGATGGTGGGCCGGA
TCCGGCCCACCATCACCGAGAAGTACGATGGGAGCGTCAACCCCACCGAGTTTCTCCAGGTCTATACGACCGGGATCGAGGCCGCTGGGGGTGACGACAG[G/A]
GTCATGGCGAACTTCTTTCCCATGGCCCTAAAAGGACAGGCGCGGGGTTGGCTAATGAACCTGCCACCCGCGTCGGTCCACTCCTGGGAAGATTTGTGCC
| 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 | 26.60% | 0.00% | 12.08% | 61.30% | NA |
| All Indica | 2759 | 3.00% | 0.00% | 7.61% | 89.42% | NA |
| All Japonica | 1512 | 68.30% | 0.10% | 16.01% | 15.54% | NA |
| Aus | 269 | 11.50% | 0.00% | 37.55% | 50.93% | NA |
| Indica I | 595 | 3.50% | 0.00% | 9.41% | 87.06% | NA |
| Indica II | 465 | 3.00% | 0.00% | 3.87% | 93.12% | NA |
| Indica III | 913 | 1.20% | 0.00% | 7.56% | 91.24% | NA |
| Indica Intermediate | 786 | 4.60% | 0.00% | 8.52% | 86.90% | NA |
| Temperate Japonica | 767 | 90.70% | 0.30% | 6.13% | 2.87% | NA |
| Tropical Japonica | 504 | 31.50% | 0.00% | 30.95% | 37.50% | NA |
| Japonica Intermediate | 241 | 73.90% | 0.00% | 16.18% | 9.96% | NA |
| VI/Aromatic | 96 | 77.10% | 0.00% | 3.12% | 19.79% | NA |
| Intermediate | 90 | 40.00% | 0.00% | 16.67% | 43.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0725420600 | C -> DEL | LOC_Os07g42460.1 | N | frameshift_variant | Average:4.601; most accessible tissue: Minghui63 flower, score: 7.958 | N | N | N | N |
| vg0725420600 | C -> T | LOC_Os07g42460.1 | synonymous_variant ; p.Arg270Arg; LOW | synonymous_codon | Average:4.601; most accessible tissue: Minghui63 flower, score: 7.958 | N | N | N | N |