| Variant ID: vg0335310116 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 35310116 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GACAAATCGACCTTTAATAAAATTTATTTTGAAAATAGACCCAAAATATTCCTTACTTCCCTAAATGTTTGACGCTGTTGACTTTTTAAAGTATGTTTAA[C/T]
CATTTGTCTTATTCAAAAACTTTTGTGAAATATGTAAAACTATATGTATATATAAAAGTATATTTAACAATAAATCAAATGATAGGAAAAGAATTAATTA
TAATTAATTCTTTTCCTATCATTTGATTTATTGTTAAATATACTTTTATATATACATATAGTTTTACATATTTCACAAAAGTTTTTGAATAAGACAAATG[G/A]
TTAAACATACTTTAAAAAGTCAACAGCGTCAAACATTTAGGGAAGTAAGGAATATTTTGGGTCTATTTTCAAAATAAATTTTATTAAAGGTCGATTTGTC
| 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 | 95.90% | 4.10% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 97.80% | 2.20% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 59.50% | 40.50% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 94.80% | 5.20% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 95.90% | 4.10% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 96.80% | 3.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 94.40% | 5.60% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0335310116 | C -> T | LOC_Os03g62330.1 | 3_prime_UTR_variant ; 193.0bp to feature; MODIFIER | silent_mutation | Average:59.444; most accessible tissue: Minghui63 root, score: 79.74 | N | N | N | N |
| vg0335310116 | C -> T | LOC_Os03g62314.1 | upstream_gene_variant ; 730.0bp to feature; MODIFIER | silent_mutation | Average:59.444; most accessible tissue: Minghui63 root, score: 79.74 | N | N | N | N |
| vg0335310116 | C -> T | LOC_Os03g62340.1 | downstream_gene_variant ; 2335.0bp to feature; MODIFIER | silent_mutation | Average:59.444; most accessible tissue: Minghui63 root, score: 79.74 | N | N | N | N |