| Variant ID: vg1224819418 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr12 | Position: 24819418 |
| Reference Allele: GAA | Alternative Allele: G |
| Primary Allele: GAA | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
CGGTATGCTCTGAGATGAAAACAATAATCTGGTTAACTTCGTTAGATGATACTCCAACTATAGTTGGCATGTTGAATGTTGTGTCCAGATAACAGTGACT[GAA/G]
AGTCTGAAATTCTACACAGAAAAACGCTGATTTTTGCAGGATGATTTTTGGAATGGAAATTTTTGCAGGATGATTAAACTTCTCTGCAATGCCACTTTGA
TCAAAGTGGCATTGCAGAGAAGTTTAATCATCCTGCAAAAATTTCCATTCCAAAAATCATCCTGCAAAAATCAGCGTTTTTCTGTGTAGAATTTCAGACT[TTC/C]
AGTCACTGTTATCTGGACACAACATTCAACATGCCAACTATAGTTGGAGTATCATCTAACGAAGTTAACCAGATTATTGTTTTCATCTCAGAGCATACCG
| Populations | Population Size | Frequency of GAA(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 93.80% | 6.20% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 84.50% | 15.50% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.50% | 0.50% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 93.90% | 6.10% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 88.30% | 11.70% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 46.90% | 53.10% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 47.90% | 52.10% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 92.20% | 7.80% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1224819418 | GAA -> G | LOC_Os12g40130.1 | upstream_gene_variant ; 1685.0bp to feature; MODIFIER | silent_mutation | Average:52.171; most accessible tissue: Zhenshan97 panicle, score: 76.605 | N | N | N | N |
| vg1224819418 | GAA -> G | LOC_Os12g40140.1 | upstream_gene_variant ; 3851.0bp to feature; MODIFIER | silent_mutation | Average:52.171; most accessible tissue: Zhenshan97 panicle, score: 76.605 | N | N | N | N |
| vg1224819418 | GAA -> G | LOC_Os12g40115.1 | downstream_gene_variant ; 2042.0bp to feature; MODIFIER | silent_mutation | Average:52.171; most accessible tissue: Zhenshan97 panicle, score: 76.605 | N | N | N | N |
| vg1224819418 | GAA -> G | LOC_Os12g40120.1 | intron_variant ; MODIFIER | silent_mutation | Average:52.171; most accessible tissue: Zhenshan97 panicle, score: 76.605 | N | N | N | N |