| Variant ID: vg0430653768 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 30653768 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 404. )
CACTAGTGAATTGGGTGCCATTATCCGTAATGATACGGTTAGGCACTCCAAAACGGGCCGTGATGCCCTTAATGAATTTAAGTGCAGAGTGCTTATCGAT[C/T]
TTGACGACCGGATAAGCCTCGGGCCACTTAGTGAACTTGTCGATCGCGACATACAGATACTCAAACCCGCCCGGGGCCCGCTTAAACGGTCCCAGGATAT
ATATCCTGGGACCGTTTAAGCGGGCCCCGGGCGGGTTTGAGTATCTGTATGTCGCGATCGACAAGTTCACTAAGTGGCCCGAGGCTTATCCGGTCGTCAA[G/A]
ATCGATAAGCACTCTGCACTTAAATTCATTAAGGGCATCACGGCCCGTTTTGGAGTGCCTAACCGTATCATTACGGATAATGGCACCCAATTCACTAGTG
| 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 | 65.70% | 0.10% | 15.72% | 18.45% | NA |
| All Indica | 2759 | 71.80% | 0.10% | 23.60% | 4.53% | NA |
| All Japonica | 1512 | 51.50% | 0.00% | 3.70% | 44.84% | NA |
| Aus | 269 | 82.90% | 0.00% | 5.95% | 11.15% | NA |
| Indica I | 595 | 46.70% | 0.20% | 48.07% | 5.04% | NA |
| Indica II | 465 | 77.40% | 0.00% | 18.71% | 3.87% | NA |
| Indica III | 913 | 88.80% | 0.20% | 8.98% | 1.97% | NA |
| Indica Intermediate | 786 | 67.60% | 0.00% | 24.94% | 7.51% | NA |
| Temperate Japonica | 767 | 64.70% | 0.00% | 0.52% | 34.81% | NA |
| Tropical Japonica | 504 | 35.10% | 0.00% | 8.73% | 56.15% | NA |
| Japonica Intermediate | 241 | 43.60% | 0.00% | 3.32% | 53.11% | NA |
| VI/Aromatic | 96 | 61.50% | 2.10% | 7.29% | 29.17% | NA |
| Intermediate | 90 | 73.30% | 0.00% | 14.44% | 12.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0430653768 | C -> DEL | LOC_Os04g51730.1 | N | frameshift_variant | Average:11.246; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |
| vg0430653768 | C -> T | LOC_Os04g51730.1 | synonymous_variant ; p.Lys198Lys; LOW | synonymous_codon | Average:11.246; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |