| Variant ID: vg0512021423 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 12021423 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GAGCGTCTGCTACAACATTAGCCTTTCCCGGATGATAATGAATTCCCATGTCATAATCCTTAATTAATTCCAACCATCTCCGTTGTCTCATGTTCAGATC[C/T]
GGCTGAGTAAAGATATACTTTAAACTCTTGTGATCGGTGTACACTTCTGTACGAGTACCGAAAAGATAATGACGCCAAATCTTCAATGCATGAACGACTG
CAGTCGTTCATGCATTGAAGATTTGGCGTCATTATCTTTTCGGTACTCGTACAGAAGTGTACACCGATCACAAGAGTTTAAAGTATATCTTTACTCAGCC[G/A]
GATCTGAACATGAGACAACGGAGATGGTTGGAATTAATTAAGGATTATGACATGGGAATTCATTATCATCCGGGAAAGGCTAATGTTGTAGCAGACGCTC
| 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 | 87.20% | 0.10% | 3.70% | 8.97% | NA |
| All Indica | 2759 | 86.90% | 0.00% | 4.17% | 8.92% | NA |
| All Japonica | 1512 | 98.50% | 0.50% | 0.66% | 0.33% | NA |
| Aus | 269 | 21.90% | 0.00% | 15.99% | 62.08% | NA |
| Indica I | 595 | 91.30% | 0.00% | 3.53% | 5.21% | NA |
| Indica II | 465 | 97.80% | 0.00% | 0.86% | 1.29% | NA |
| Indica III | 913 | 79.10% | 0.00% | 7.89% | 13.03% | NA |
| Indica Intermediate | 786 | 86.30% | 0.00% | 2.29% | 11.45% | NA |
| Temperate Japonica | 767 | 98.60% | 0.70% | 0.78% | 0.00% | NA |
| Tropical Japonica | 504 | 98.40% | 0.20% | 0.60% | 0.79% | NA |
| Japonica Intermediate | 241 | 98.80% | 0.40% | 0.41% | 0.41% | NA |
| VI/Aromatic | 96 | 95.80% | 0.00% | 3.12% | 1.04% | NA |
| Intermediate | 90 | 90.00% | 0.00% | 4.44% | 5.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0512021423 | C -> T | LOC_Os05g20480.1 | synonymous_variant ; p.Pro680Pro; LOW | synonymous_codon | Average:9.129; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |
| vg0512021423 | C -> DEL | LOC_Os05g20480.1 | N | frameshift_variant | Average:9.129; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |