| Variant ID: vg0335310007 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 35310007 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CCGAAATGAAGGAAATGATGCCTCAGTGCTCAGTGCTTACTTTAGTACTCTCTATTCTATGAATTTAGACACGTAAAGCACATATATACATCAAAACAGC[C/T]
GAAATTCTGACAAATCGACCTTTAATAAAATTTATTTTGAAAATAGACCCAAAATATTCCTTACTTCCCTAAATGTTTGACGCTGTTGACTTTTTAAAGT
ACTTTAAAAAGTCAACAGCGTCAAACATTTAGGGAAGTAAGGAATATTTTGGGTCTATTTTCAAAATAAATTTTATTAAAGGTCGATTTGTCAGAATTTC[G/A]
GCTGTTTTGATGTATATATGTGCTTTACGTGTCTAAATTCATAGAATAGAGAGTACTAAAGTAAGCACTGAGCACTGAGGCATCATTTCCTTCATTTCGG
| 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 | 96.70% | 3.30% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 94.30% | 5.70% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica II | 465 | 98.10% | 1.90% | 0.00% | 0.00% | NA |
| Indica III | 913 | 86.20% | 13.80% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 97.20% | 2.80% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | 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 | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0335310007 | C -> T | LOC_Os03g62330.1 | 3_prime_UTR_variant ; 302.0bp to feature; MODIFIER | silent_mutation | Average:66.805; most accessible tissue: Minghui63 root, score: 80.951 | N | N | N | N |
| vg0335310007 | C -> T | LOC_Os03g62314.1 | upstream_gene_variant ; 621.0bp to feature; MODIFIER | silent_mutation | Average:66.805; most accessible tissue: Minghui63 root, score: 80.951 | N | N | N | N |
| vg0335310007 | C -> T | LOC_Os03g62340.1 | downstream_gene_variant ; 2444.0bp to feature; MODIFIER | silent_mutation | Average:66.805; most accessible tissue: Minghui63 root, score: 80.951 | N | N | N | N |