| Variant ID: vg0318604727 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr03 | Position: 18604727 |
| Reference Allele: C | Alternative Allele: CAG |
| Primary Allele: C | Secondary Allele: CAG |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 313. )
TGCAGCCTGAAATCTCTTGAACAAACTAGTACCGTACCTAATGGATACATTAGTATTATTTAGAATGTTGTAAAACCTTACATCCAGAGTATGTATAGAA[C/CAG]
AGAGAGAGAGAGAGATCTTACCCTAACTTCTGAGCAGTAGATGAAATTACAGTTGCAGGCAACTGAACTGGGTCACCAACCTGACAAAATATTAACAGAA
TTCTGTTAATATTTTGTCAGGTTGGTGACCCAGTTCAGTTGCCTGCAACTGTAATTTCATCTACTGCTCAGAAGTTAGGGTAAGATCTCTCTCTCTCTCT[G/CTG]
TTCTATACATACTCTGGATGTAAGGTTTTACAACATTCTAAATAATACTAATGTATCCATTAGGTACGGTACTAGTTTGTTCAAGAGATTTCAGGCTGCA
| Populations | Population Size | Frequency of C(primary allele) | Frequency of CAG(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 72.30% | 4.00% | 17.90% | 5.78% | NA |
| All Indica | 2759 | 65.10% | 4.30% | 26.71% | 3.81% | NA |
| All Japonica | 1512 | 87.60% | 0.20% | 1.52% | 10.71% | NA |
| Aus | 269 | 48.30% | 23.00% | 28.62% | 0.00% | NA |
| Indica I | 595 | 41.80% | 6.70% | 39.50% | 11.93% | NA |
| Indica II | 465 | 43.70% | 3.70% | 50.97% | 1.72% | NA |
| Indica III | 913 | 90.60% | 1.00% | 8.21% | 0.22% | NA |
| Indica Intermediate | 786 | 65.90% | 6.90% | 24.17% | 3.05% | NA |
| Temperate Japonica | 767 | 99.90% | 0.00% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 69.40% | 0.00% | 1.79% | 28.77% | NA |
| Japonica Intermediate | 241 | 86.30% | 1.20% | 5.39% | 7.05% | NA |
| VI/Aromatic | 96 | 96.90% | 1.00% | 2.08% | 0.00% | NA |
| Intermediate | 90 | 82.20% | 3.30% | 7.78% | 6.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0318604727 | C -> DEL | N | N | silent_mutation | Average:14.26; most accessible tissue: Zhenshan97 panicle, score: 20.424 | N | N | N | N |
| vg0318604727 | C -> CAG | LOC_Os03g32526.1 | intron_variant ; MODIFIER | silent_mutation | Average:14.26; most accessible tissue: Zhenshan97 panicle, score: 20.424 | N | N | N | N |