| Variant ID: vg0509254308 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 9254308 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TTTGTAATTAGACTTAGTATATAATTATTTACTAGCTAGGGTTGTATAATATACGTCACCTAGACTTAGCTTATATCACGATTTGTAATTAGACTTAGCA[C/T]
GTAAGGTTGTGTAGGGTTCTAATGTACGACATTTACACTTAGCATACATGACTTAGATTGTTAAAACATAAATGTCTCGTGACTTAGCAGATGTTTCTTG
CAAGAAACATCTGCTAAGTCACGAGACATTTATGTTTTAACAATCTAAGTCATGTATGCTAAGTGTAAATGTCGTACATTAGAACCCTACACAACCTTAC[G/A]
TGCTAAGTCTAATTACAAATCGTGATATAAGCTAAGTCTAGGTGACGTATATTATACAACCCTAGCTAGTAAATAATTATATACTAAGTCTAATTACAAA
| 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 | 92.50% | 0.20% | 1.99% | 5.29% | NA |
| All Indica | 2759 | 90.10% | 0.40% | 3.15% | 6.38% | NA |
| All Japonica | 1512 | 99.90% | 0.00% | 0.00% | 0.07% | NA |
| Aus | 269 | 72.10% | 0.00% | 2.23% | 25.65% | NA |
| Indica I | 595 | 94.10% | 0.00% | 1.68% | 4.20% | NA |
| Indica II | 465 | 79.60% | 0.20% | 5.81% | 14.41% | NA |
| Indica III | 913 | 90.00% | 0.80% | 3.83% | 5.37% | NA |
| Indica Intermediate | 786 | 93.30% | 0.40% | 1.91% | 4.45% | NA |
| Temperate Japonica | 767 | 99.90% | 0.00% | 0.00% | 0.13% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 0.00% | 1.04% | NA |
| Intermediate | 90 | 95.60% | 0.00% | 1.11% | 3.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0509254308 | C -> T | LOC_Os05g16330.1 | downstream_gene_variant ; 2648.0bp to feature; MODIFIER | silent_mutation | Average:19.293; most accessible tissue: Zhenshan97 panicle, score: 36.038 | N | N | N | N |
| vg0509254308 | C -> T | LOC_Os05g16340.1 | intron_variant ; MODIFIER | silent_mutation | Average:19.293; most accessible tissue: Zhenshan97 panicle, score: 36.038 | N | N | N | N |
| vg0509254308 | C -> DEL | N | N | silent_mutation | Average:19.293; most accessible tissue: Zhenshan97 panicle, score: 36.038 | N | N | N | N |