| Variant ID: vg0620602566 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 20602566 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
ATTTATCTTGTGAGAATTATCTCTTGGTTAGTTCCTAAATAGCATACGGGATTATTGTTCACTATAATCAACTAAAATATAGTGATTGCTTTAGTGAGTT[A/G]
TAAACACTAAAGTAGATATTAATTGCTTAGACGTAGTGTTTAGGTAATTGTTATACAGTAATTGTTGCAACTTCTTTTTGAGCTGTCTGCTCCTCGGGGC
GCCCCGAGGAGCAGACAGCTCAAAAAGAAGTTGCAACAATTACTGTATAACAATTACCTAAACACTACGTCTAAGCAATTAATATCTACTTTAGTGTTTA[T/C]
AACTCACTAAAGCAATCACTATATTTTAGTTGATTATAGTGAACAATAATCCCGTATGCTATTTAGGAACTAACCAAGAGATAATTCTCACAAGATAAAT
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 98.30% | 0.40% | 0.17% | 1.18% | NA |
| All Indica | 2759 | 99.00% | 0.60% | 0.29% | 0.07% | NA |
| All Japonica | 1512 | 96.60% | 0.00% | 0.00% | 3.44% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 97.60% | 1.80% | 0.50% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.70% | 0.00% | 0.22% | 0.11% | NA |
| Indica Intermediate | 786 | 98.70% | 0.80% | 0.38% | 0.13% | NA |
| Temperate Japonica | 767 | 99.20% | 0.00% | 0.00% | 0.78% | NA |
| Tropical Japonica | 504 | 99.00% | 0.00% | 0.00% | 0.99% | NA |
| Japonica Intermediate | 241 | 83.00% | 0.00% | 0.00% | 17.01% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 96.70% | 1.10% | 0.00% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0620602566 | A -> G | LOC_Os06g35340.1 | intron_variant ; MODIFIER | silent_mutation | Average:15.673; most accessible tissue: Zhenshan97 root, score: 20.427 | N | N | N | N |
| vg0620602566 | A -> DEL | N | N | silent_mutation | Average:15.673; most accessible tissue: Zhenshan97 root, score: 20.427 | N | N | N | N |