| Variant ID: vg0415575620 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 15575620 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
ACCTGGACTAAAGATCTAGAAGATTTTTAATCCCAGTTGGTATTACCAACCGGGACTAAAATTCAACGCTTAATATATAATCCTTCTTCCCTATCCTCTC[C/A]
TCCACAACCGCCTCACACTTATCCTCTCAGATCGATCTCCCTCTTCTCCCTCTCAGATCGATCTCCCTCTCCTCCTCCCCCTCCGCCACCTCCACTACCT
AGGTAGTGGAGGTGGCGGAGGGGGAGGAGGAGAGGGAGATCGATCTGAGAGGGAGAAGAGGGAGATCGATCTGAGAGGATAAGTGTGAGGCGGTTGTGGA[G/T]
GAGAGGATAGGGAAGAAGGATTATATATTAAGCGTTGAATTTTAGTCCCGGTTGGTAATACCAACTGGGATTAAAAATCTTCTAGATCTTTAGTCCAGGT
| 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 | 71.10% | 6.60% | 0.53% | 21.75% | NA |
| All Indica | 2759 | 72.70% | 11.10% | 0.51% | 15.66% | NA |
| All Japonica | 1512 | 78.30% | 0.00% | 0.60% | 21.10% | NA |
| Aus | 269 | 5.60% | 0.00% | 0.00% | 94.42% | NA |
| Indica I | 595 | 90.40% | 0.30% | 0.50% | 8.74% | NA |
| Indica II | 465 | 68.80% | 4.30% | 0.22% | 26.67% | NA |
| Indica III | 913 | 59.80% | 24.40% | 0.88% | 14.90% | NA |
| Indica Intermediate | 786 | 76.60% | 7.90% | 0.25% | 15.27% | NA |
| Temperate Japonica | 767 | 59.80% | 0.00% | 0.78% | 39.37% | NA |
| Tropical Japonica | 504 | 98.80% | 0.00% | 0.20% | 0.99% | NA |
| Japonica Intermediate | 241 | 94.20% | 0.00% | 0.83% | 4.98% | NA |
| VI/Aromatic | 96 | 91.70% | 0.00% | 0.00% | 8.33% | NA |
| Intermediate | 90 | 76.70% | 4.40% | 2.22% | 16.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0415575620 | C -> DEL | N | N | silent_mutation | Average:32.198; most accessible tissue: Zhenshan97 flag leaf, score: 49.013 | N | N | N | N |
| vg0415575620 | C -> A | LOC_Os04g26690.1 | intron_variant ; MODIFIER | silent_mutation | Average:32.198; most accessible tissue: Zhenshan97 flag leaf, score: 49.013 | N | N | N | N |