| Variant ID: vg0811598961 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 11598961 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GAAAAGTTATTAAGATTGGCGGGGGCCTGGGGGCTCACTCCGACGCGCCCGGGTCGCCGGCCTCGTCGTTGCTGTCGTCCGCACCATCGTCACCGCCCTC[C/T]
TCGTCGGAGTCGAGGGCGAACGCGAGCTGAGGGGCCGTACCCTCGAAGCTGTGGACGATGTGGTCGGCGGCGTCCCGGACCTGCGCGCGCGCGCCGTCCT
AGGACGGCGCGCGCGCGCAGGTCCGGGACGCCGCCGACCACATCGTCCACAGCTTCGAGGGTACGGCCCCTCAGCTCGCGTTCGCCCTCGACTCCGACGA[G/A]
GAGGGCGGTGACGATGGTGCGGACGACAGCAACGACGAGGCCGGCGACCCGGGCGCGTCGGAGTGAGCCCCCAGGCCCCCGCCAATCTTAATAACTTTTC
| 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 | 34.90% | 0.30% | 4.27% | 60.60% | NA |
| All Indica | 2759 | 22.10% | 0.40% | 3.95% | 73.50% | NA |
| All Japonica | 1512 | 57.50% | 0.00% | 5.22% | 37.24% | NA |
| Aus | 269 | 39.40% | 0.00% | 2.97% | 57.62% | NA |
| Indica I | 595 | 12.10% | 0.20% | 2.02% | 85.71% | NA |
| Indica II | 465 | 11.00% | 0.00% | 3.01% | 86.02% | NA |
| Indica III | 913 | 37.20% | 0.80% | 6.57% | 55.42% | NA |
| Indica Intermediate | 786 | 18.70% | 0.50% | 2.93% | 77.86% | NA |
| Temperate Japonica | 767 | 84.70% | 0.00% | 0.26% | 14.99% | NA |
| Tropical Japonica | 504 | 26.40% | 0.00% | 10.32% | 63.29% | NA |
| Japonica Intermediate | 241 | 36.10% | 0.00% | 10.37% | 53.53% | NA |
| VI/Aromatic | 96 | 29.20% | 0.00% | 5.21% | 65.62% | NA |
| Intermediate | 90 | 37.80% | 0.00% | 1.11% | 61.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0811598961 | C -> T | LOC_Os08g19400.1 | synonymous_variant ; p.Glu314Glu; LOW | synonymous_codon | Average:17.049; most accessible tissue: Zhenshan97 flower, score: 29.832 | N | N | N | N |
| vg0811598961 | C -> DEL | LOC_Os08g19400.1 | N | frameshift_variant | Average:17.049; most accessible tissue: Zhenshan97 flower, score: 29.832 | N | N | N | N |