| Variant ID: vg0521976503 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 21976503 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
TGTTTTTTGTAAACTACATTTTCAGTTAGTAGTAGTATATGCTATTTTTAAATATAGTGTCTCCAATACAGAAATTTGGTCCCTTCACTGGATTGGACAG[A/C]
AGGAAACCCATATGAAAAAGAAGGAGCTGGGATACCGATGGAAAGGTTTGTATCAACATGTTACGGATTTTTACGATTTTTTTTGAGCCAGGATATTGGT
ACCAATATCCTGGCTCAAAAAAAATCGTAAAAATCCGTAACATGTTGATACAAACCTTTCCATCGGTATCCCAGCTCCTTCTTTTTCATATGGGTTTCCT[T/G]
CTGTCCAATCCAGTGAAGGGACCAAATTTCTGTATTGGAGACACTATATTTAAAAATAGCATATACTACTACTAACTGAAAATGTAGTTTACAAAAAACA
| Populations | Population Size | Frequency of A(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 87.10% | 0.40% | 8.29% | 4.21% | NA |
| All Indica | 2759 | 79.40% | 0.00% | 13.88% | 6.71% | NA |
| All Japonica | 1512 | 98.10% | 1.10% | 0.26% | 0.46% | NA |
| Aus | 269 | 97.80% | 0.00% | 1.12% | 1.12% | NA |
| Indica I | 595 | 73.40% | 0.00% | 13.45% | 13.11% | NA |
| Indica II | 465 | 88.20% | 0.00% | 8.60% | 3.23% | NA |
| Indica III | 913 | 75.10% | 0.00% | 19.17% | 5.70% | NA |
| Indica Intermediate | 786 | 83.70% | 0.00% | 11.20% | 5.09% | NA |
| Temperate Japonica | 767 | 99.10% | 0.00% | 0.13% | 0.78% | NA |
| Tropical Japonica | 504 | 96.20% | 3.40% | 0.40% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.00% | 0.41% | 0.41% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 93.30% | 0.00% | 2.22% | 4.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0521976503 | A -> DEL | LOC_Os05g37540.1 | N | frameshift_variant | Average:6.806; most accessible tissue: Callus, score: 18.902 | N | N | N | N |
| vg0521976503 | A -> C | LOC_Os05g37540.1 | missense_variant ; p.Glu85Ala; MODERATE | nonsynonymous_codon ; E85A | Average:6.806; most accessible tissue: Callus, score: 18.902 | unknown | unknown | TOLERATED | 0.16 |