| Variant ID: vg0620602558 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 20602558 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
TAATTTAGATTTATCTTGTGAGAATTATCTCTTGGTTAGTTCCTAAATAGCATACGGGATTATTGTTCACTATAATCAACTAAAATATAGTGATTGCTTT[A/G]
GTGAGTTATAAACACTAAAGTAGATATTAATTGCTTAGACGTAGTGTTTAGGTAATTGTTATACAGTAATTGTTGCAACTTCTTTTTGAGCTGTCTGCTC
GAGCAGACAGCTCAAAAAGAAGTTGCAACAATTACTGTATAACAATTACCTAAACACTACGTCTAAGCAATTAATATCTACTTTAGTGTTTATAACTCAC[T/C]
AAAGCAATCACTATATTTTAGTTGATTATAGTGAACAATAATCCCGTATGCTATTTAGGAACTAACCAAGAGATAATTCTCACAAGATAAATCTAAATTA
| 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 | 13.20% | 5.20% | 63.80% | 17.80% | NA |
| All Indica | 2759 | 0.30% | 5.60% | 69.55% | 24.50% | NA |
| All Japonica | 1512 | 40.00% | 3.20% | 47.29% | 9.52% | NA |
| Aus | 269 | 0.00% | 12.60% | 85.87% | 1.49% | NA |
| Indica I | 595 | 0.70% | 4.00% | 49.58% | 45.71% | NA |
| Indica II | 465 | 0.40% | 5.60% | 69.46% | 24.52% | NA |
| Indica III | 913 | 0.00% | 6.50% | 84.12% | 9.42% | NA |
| Indica Intermediate | 786 | 0.40% | 5.90% | 67.81% | 25.95% | NA |
| Temperate Japonica | 767 | 71.80% | 2.00% | 21.64% | 4.56% | NA |
| Tropical Japonica | 504 | 3.40% | 5.00% | 86.31% | 5.36% | NA |
| Japonica Intermediate | 241 | 15.40% | 3.30% | 47.30% | 34.02% | NA |
| VI/Aromatic | 96 | 0.00% | 5.20% | 94.79% | 0.00% | NA |
| Intermediate | 90 | 11.10% | 4.40% | 65.56% | 18.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0620602558 | A -> G | LOC_Os06g35340.1 | intron_variant ; MODIFIER | silent_mutation | Average:15.478; most accessible tissue: Zhenshan97 root, score: 20.427 | N | N | N | N |
| vg0620602558 | A -> DEL | N | N | silent_mutation | Average:15.478; most accessible tissue: Zhenshan97 root, score: 20.427 | N | N | N | N |