| Variant ID: vg0610041845 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 10041845 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GGTTCCCCTCCGCATCCCTCTCCACGTTCCCTTCCTCGTTCAAGTACTGGTTTGGATCCTCGTTCCCCTCTTCTTCATTCCAGTACTGGCTGCTTCCCTC[C/T]
GCGATTGTATCGTACAATATCTGTTCCTCATCGCGGTCAGCCATCTGTTGATACAAGAAACATCTGCTAAGTCACGAGACATTTATGTTTTAACAATCTA
TAGATTGTTAAAACATAAATGTCTCGTGACTTAGCAGATGTTTCTTGTATCAACAGATGGCTGACCGCGATGAGGAACAGATATTGTACGATACAATCGC[G/A]
GAGGGAAGCAGCCAGTACTGGAATGAAGAAGAGGGGAACGAGGATCCAAACCAGTACTTGAACGAGGAAGGGAACGTGGAGAGGGATGCGGAGGGGAACC
| 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 | 27.50% | 0.10% | 12.27% | 60.16% | NA |
| All Indica | 2759 | 31.00% | 0.00% | 13.85% | 55.16% | NA |
| All Japonica | 1512 | 19.60% | 0.10% | 9.39% | 70.90% | NA |
| Aus | 269 | 35.30% | 1.50% | 15.61% | 47.58% | NA |
| Indica I | 595 | 18.20% | 0.00% | 15.46% | 66.39% | NA |
| Indica II | 465 | 18.10% | 0.00% | 4.73% | 77.20% | NA |
| Indica III | 913 | 48.80% | 0.00% | 17.85% | 33.30% | NA |
| Indica Intermediate | 786 | 27.60% | 0.00% | 13.36% | 59.03% | NA |
| Temperate Japonica | 767 | 26.20% | 0.00% | 16.43% | 57.37% | NA |
| Tropical Japonica | 504 | 12.90% | 0.00% | 0.99% | 86.11% | NA |
| Japonica Intermediate | 241 | 12.90% | 0.40% | 4.56% | 82.16% | NA |
| VI/Aromatic | 96 | 32.30% | 0.00% | 4.17% | 63.54% | NA |
| Intermediate | 90 | 22.20% | 0.00% | 11.11% | 66.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0610041845 | C -> T | LOC_Os06g17330.1 | synonymous_variant ; p.Ala15Ala; LOW | synonymous_codon | Average:6.786; most accessible tissue: Minghui63 root, score: 15.664 | N | N | N | N |
| vg0610041845 | C -> DEL | LOC_Os06g17330.1 | N | frameshift_variant | Average:6.786; most accessible tissue: Minghui63 root, score: 15.664 | N | N | N | N |