| Variant ID: vg0128724176 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 28724176 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
TTTGCAATGGCCGCTGTCCGAATGACCCTCCGATGGGATGGGTCATACCTACCTCCACTTCGCTGGAAGCAGATGCAACGTGGGAGCACGGTTTGTCTGC[T/C]
GATGACGTGACCGGCGTCAGACCAGTCACAGACCGGTCATTCTTGTCCACCACGTGTCAGTTTAGCATGTCGCACGTCTGTCCTTCTTCATACAATGACT
AGTCATTGTATGAAGAAGGACAGACGTGCGACATGCTAAACTGACACGTGGTGGACAAGAATGACCGGTCTGTGACTGGTCTGACGCCGGTCACGTCATC[A/G]
GCAGACAAACCGTGCTCCCACGTTGCATCTGCTTCCAGCGAAGTGGAGGTAGGTATGACCCATCCCATCGGAGGGTCATTCGGACAGCGGCCATTGCAAA
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 33.50% | 1.00% | 15.68% | 49.83% | NA |
| All Indica | 2759 | 7.40% | 1.50% | 23.34% | 67.78% | NA |
| All Japonica | 1512 | 85.80% | 0.10% | 1.06% | 13.03% | NA |
| Aus | 269 | 9.30% | 0.40% | 20.07% | 70.26% | NA |
| Indica I | 595 | 2.70% | 2.00% | 15.46% | 79.83% | NA |
| Indica II | 465 | 4.50% | 1.70% | 11.83% | 81.94% | NA |
| Indica III | 913 | 11.30% | 1.00% | 37.02% | 50.71% | NA |
| Indica Intermediate | 786 | 8.00% | 1.70% | 20.23% | 70.10% | NA |
| Temperate Japonica | 767 | 99.30% | 0.00% | 0.00% | 0.65% | NA |
| Tropical Japonica | 504 | 61.70% | 0.40% | 3.17% | 34.72% | NA |
| Japonica Intermediate | 241 | 92.90% | 0.00% | 0.00% | 7.05% | NA |
| VI/Aromatic | 96 | 15.60% | 1.00% | 13.54% | 69.79% | NA |
| Intermediate | 90 | 48.90% | 0.00% | 15.56% | 35.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0128724176 | T -> DEL | LOC_Os01g49990.1 | N | frameshift_variant | Average:10.888; most accessible tissue: Callus, score: 22.262 | N | N | N | N |
| vg0128724176 | T -> C | LOC_Os01g49990.1 | synonymous_variant ; p.Ala23Ala; LOW | synonymous_codon | Average:10.888; most accessible tissue: Callus, score: 22.262 | N | N | N | N |