| Variant ID: vg0811599230 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 11599230 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GCCAGTACGAGCTCCACCGCCCCCCGGGCGAGGTCCCTCGAGGATGACTTGATCGTCTCCTCGAGCTCCTCGGGGAGCCGCTTGAGGGTCCCGGCCATCT[C/T]
TGAGAGGCGCTGGGCGAGGCCCCCCTGGTTGGCGGCGTACTTCGCGTACCGCCCGCCCCAGAGGCCCGCCTGCCGCCCGGCACGGTCTAGACGGGAGACG
CGTCTCCCGTCTAGACCGTGCCGGGCGGCAGGCGGGCCTCTGGGGCGGGCGGTACGCGAAGTACGCCGCCAACCAGGGGGGCCTCGCCCAGCGCCTCTCA[G/A]
AGATGGCCGGGACCCTCAAGCGGCTCCCCGAGGAGCTCGAGGAGACGATCAAGTCATCCTCGAGGGACCTCGCCCGGGGGGCGGTGGAGCTCGTACTGGC
| 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 | 47.80% | 0.50% | 2.71% | 48.96% | NA |
| All Indica | 2759 | 54.00% | 0.10% | 1.99% | 43.97% | NA |
| All Japonica | 1512 | 36.40% | 1.10% | 4.23% | 58.27% | NA |
| Aus | 269 | 50.60% | 1.50% | 1.86% | 46.10% | NA |
| Indica I | 595 | 32.90% | 0.00% | 3.87% | 63.19% | NA |
| Indica II | 465 | 37.20% | 0.00% | 2.15% | 60.65% | NA |
| Indica III | 913 | 78.40% | 0.10% | 0.99% | 20.48% | NA |
| Indica Intermediate | 786 | 51.40% | 0.10% | 1.65% | 46.82% | NA |
| Temperate Japonica | 767 | 27.20% | 0.10% | 6.00% | 66.62% | NA |
| Tropical Japonica | 504 | 48.20% | 2.20% | 2.78% | 46.83% | NA |
| Japonica Intermediate | 241 | 40.70% | 2.10% | 1.66% | 55.60% | NA |
| VI/Aromatic | 96 | 47.90% | 2.10% | 1.04% | 48.96% | NA |
| Intermediate | 90 | 42.20% | 0.00% | 3.33% | 54.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0811599230 | C -> T | LOC_Os08g19400.1 | missense_variant ; p.Glu225Lys; MODERATE | nonsynonymous_codon ; E225K | Average:20.42; most accessible tissue: Zhenshan97 flag leaf, score: 39.979 | unknown | unknown | TOLERATED | 0.36 |
| vg0811599230 | C -> DEL | LOC_Os08g19400.1 | N | frameshift_variant | Average:20.42; most accessible tissue: Zhenshan97 flag leaf, score: 39.979 | N | N | N | N |