| Variant ID: vg0811599210 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 11599210 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GGTCCCTGGCCTGGTAGCTTGCCAGTACGAGCTCCACCGCCCCCCGGGCGAGGTCCCTCGAGGATGACTTGATCGTCTCCTCGAGCTCCTCGGGGAGCCG[C/A]
TTGAGGGTCCCGGCCATCTCTGAGAGGCGCTGGGCGAGGCCCCCCTGGTTGGCGGCGTACTTCGCGTACCGCCCGCCCCAGAGGCCCGCCTGCCGCCCGG
CCGGGCGGCAGGCGGGCCTCTGGGGCGGGCGGTACGCGAAGTACGCCGCCAACCAGGGGGGCCTCGCCCAGCGCCTCTCAGAGATGGCCGGGACCCTCAA[G/T]
CGGCTCCCCGAGGAGCTCGAGGAGACGATCAAGTCATCCTCGAGGGACCTCGCCCGGGGGGCGGTGGAGCTCGTACTGGCAAGCTACCAGGCCAGGGACC
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 47.90% | 0.40% | 2.77% | 48.96% | NA |
| All Indica | 2759 | 53.90% | 0.10% | 1.96% | 44.00% | NA |
| All Japonica | 1512 | 36.70% | 0.70% | 4.37% | 58.20% | NA |
| Aus | 269 | 50.60% | 1.50% | 1.86% | 46.10% | NA |
| Indica I | 595 | 32.80% | 0.00% | 3.87% | 63.36% | NA |
| Indica II | 465 | 37.40% | 0.00% | 1.94% | 60.65% | NA |
| Indica III | 913 | 78.30% | 0.10% | 1.10% | 20.48% | NA |
| Indica Intermediate | 786 | 51.40% | 0.30% | 1.53% | 46.82% | NA |
| Temperate Japonica | 767 | 27.50% | 0.10% | 5.74% | 66.62% | NA |
| Tropical Japonica | 504 | 48.80% | 1.20% | 3.37% | 46.63% | NA |
| Japonica Intermediate | 241 | 40.70% | 1.70% | 2.07% | 55.60% | NA |
| VI/Aromatic | 96 | 47.90% | 0.00% | 3.12% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0811599210 | C -> A | LOC_Os08g19400.1 | missense_variant ; p.Lys231Asn; MODERATE | nonsynonymous_codon ; K231N | Average:21.61; most accessible tissue: Zhenshan97 flag leaf, score: 39.979 | unknown | unknown | DELETERIOUS | 0.00 |
| vg0811599210 | C -> DEL | LOC_Os08g19400.1 | N | frameshift_variant | Average:21.61; most accessible tissue: Zhenshan97 flag leaf, score: 39.979 | N | N | N | N |