| Variant ID: vg1212722627 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 12722627 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TTAGAAACTTGTCAATGGTGGGTTGTGAGCACATGGTTTTGAAGGTCGTGCTCATGGCAATTAAAGACAGGTTCGTGAGCTACTGTTGTGAGACATTAAC[C/T]
GTGCCAACCACAAGCCAGCGTAGGCAACGGCTTTACCTTTTGTATAGCATGATTCATTACGGGGTGCCAGACTGATAAGCGGTGAGAAGTCCGTGGGGGT
ACCCCCACGGACTTCTCACCGCTTATCAGTCTGGCACCCCGTAATGAATCATGCTATACAAAAGGTAAAGCCGTTGCCTACGCTGGCTTGTGGTTGGCAC[G/A]
GTTAATGTCTCACAACAGTAGCTCACGAACCTGTCTTTAATTGCCATGAGCACGACCTTCAAAACCATGTGCTCACAACCCACCATTGACAAGTTTCTAA
| 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 | 99.20% | 0.70% | 0.11% | 0.00% | NA |
| All Indica | 2759 | 98.60% | 1.20% | 0.14% | 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 | 99.70% | 0.00% | 0.34% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 98.00% | 1.90% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 97.70% | 2.20% | 0.13% | 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 | 97.80% | 1.10% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1212722627 | C -> T | LOC_Os12g22530.1 | downstream_gene_variant ; 4173.0bp to feature; MODIFIER | silent_mutation | Average:52.041; most accessible tissue: Minghui63 panicle, score: 74.563 | N | N | N | N |
| vg1212722627 | C -> T | LOC_Os12g22540.1 | intron_variant ; MODIFIER | silent_mutation | Average:52.041; most accessible tissue: Minghui63 panicle, score: 74.563 | N | N | N | N |