| Variant ID: vg0811598906 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 11598906 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TGCAGATTAAATCAGTCTATACAAGAAGGGGGCCCGAAGGCCTCGGAAGAAGAAGGAAAAGTTATTAAGATTGGCGGGGGCCTGGGGGCTCACTCCGACG[C/T]
GCCCGGGTCGCCGGCCTCGTCGTTGCTGTCGTCCGCACCATCGTCACCGCCCTCCTCGTCGGAGTCGAGGGCGAACGCGAGCTGAGGGGCCGTACCCTCG
CGAGGGTACGGCCCCTCAGCTCGCGTTCGCCCTCGACTCCGACGAGGAGGGCGGTGACGATGGTGCGGACGACAGCAACGACGAGGCCGGCGACCCGGGC[G/A]
CGTCGGAGTGAGCCCCCAGGCCCCCGCCAATCTTAATAACTTTTCCTTCTTCTTCCGAGGCCTTCGGGCCCCCTTCTTGTATAGACTGATTTAATCTGCA
| 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 | 36.50% | 0.50% | 8.10% | 54.91% | NA |
| All Indica | 2759 | 20.90% | 0.70% | 11.13% | 67.27% | NA |
| All Japonica | 1512 | 63.80% | 0.00% | 3.84% | 32.34% | NA |
| Aus | 269 | 38.70% | 0.40% | 4.09% | 56.88% | NA |
| Indica I | 595 | 8.40% | 0.50% | 7.56% | 83.53% | NA |
| Indica II | 465 | 10.80% | 0.40% | 7.10% | 81.72% | NA |
| Indica III | 913 | 37.20% | 1.00% | 16.10% | 45.67% | NA |
| Indica Intermediate | 786 | 17.30% | 0.80% | 10.43% | 71.50% | NA |
| Temperate Japonica | 767 | 85.40% | 0.00% | 0.52% | 14.08% | NA |
| Tropical Japonica | 504 | 38.70% | 0.00% | 7.74% | 53.57% | NA |
| Japonica Intermediate | 241 | 47.70% | 0.00% | 6.22% | 46.06% | NA |
| VI/Aromatic | 96 | 44.80% | 0.00% | 3.12% | 52.08% | NA |
| Intermediate | 90 | 42.20% | 1.10% | 4.44% | 52.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0811598906 | C -> T | LOC_Os08g19400.1 | missense_variant ; p.Ala333Thr; MODERATE | nonsynonymous_codon ; A333T | Average:14.137; most accessible tissue: Zhenshan97 flower, score: 20.672 | unknown | unknown | DELETERIOUS | 0.01 |
| vg0811598906 | C -> DEL | LOC_Os08g19400.1 | N | frameshift_variant | Average:14.137; most accessible tissue: Zhenshan97 flower, score: 20.672 | N | N | N | N |