| Variant ID: vg0207034046 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 7034046 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TGTATGCAGCGAAATAGTATTATTCCTTATATAGTTAAAAGTAACTAATTTTGTTAGAACTAACTAGTCAAACATATTTGCGCGACTGAACAGACAATTA[C/T]
GCACACATATGTGAGCGAGCTTTAAAGTGTGCATTTTACTGTAAACCAAGTCAGAAACTAAGCTAGTAAAGGAAGTTGTTAATGGCAATGTCATGGGAAT
ATTCCCATGACATTGCCATTAACAACTTCCTTTACTAGCTTAGTTTCTGACTTGGTTTACAGTAAAATGCACACTTTAAAGCTCGCTCACATATGTGTGC[G/A]
TAATTGTCTGTTCAGTCGCGCAAATATGTTTGACTAGTTAGTTCTAACAAAATTAGTTACTTTTAACTATATAAGGAATAATACTATTTCGCTGCATACA
| 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 | 99.50% | 0.40% | 0.08% | 0.00% | NA |
| All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 98.50% | 1.30% | 0.26% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 99.90% | 0.00% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 96.00% | 3.80% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.00% | 0.83% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0207034046 | C -> T | LOC_Os02g13200.1 | intron_variant ; MODIFIER | silent_mutation | Average:76.057; most accessible tissue: Minghui63 flag leaf, score: 87.052 | N | N | N | N |