| Variant ID: vg0317761695 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr03 | Position: 17761695 |
| Reference Allele: TGTAGGGTGATCTTAACATAACCA | Alternative Allele: T |
| Primary Allele: TGTAGGGTGATCTTAACATA ACCA | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GTTCGACTGTGTCATCCCGATCTCTAAACTGTTGGAAATATAGTCATTAATCGGCATATTTTAATCCAAGAAAATGAAACAATGATCATGGCATAAGCAG[TGTAGGGTGATCTTAACATAACCA/T]
GTAGCATACTATGCGCATCATGAATGTCAAGAACAGGAACATACCAGTAACACGATAACATGCTAGAGGCATCATGTAGAACAGGAACAAGAACAGGAAC
GTTCCTGTTCTTGTTCCTGTTCTACATGATGCCTCTAGCATGTTATCGTGTTACTGGTATGTTCCTGTTCTTGACATTCATGATGCGCATAGTATGCTAC[TGGTTATGTTAAGATCACCCTACA/A]
CTGCTTATGCCATGATCATTGTTTCATTTTCTTGGATTAAAATATGCCGATTAATGACTATATTTCCAACAGTTTAGAGATCGGGATGACACAGTCGAAC
| Populations | Population Size | Frequency of TGTAGGGTGATCTTAACATA ACCA(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 19.40% | 11.90% | 0.76% | 67.92% | NA |
| All Indica | 2759 | 1.90% | 1.10% | 0.51% | 96.45% | NA |
| All Japonica | 1512 | 55.60% | 28.40% | 1.06% | 14.95% | NA |
| Aus | 269 | 1.10% | 1.50% | 0.37% | 97.03% | NA |
| Indica I | 595 | 1.30% | 0.50% | 1.34% | 96.81% | NA |
| Indica II | 465 | 4.30% | 0.00% | 0.22% | 95.48% | NA |
| Indica III | 913 | 0.40% | 1.40% | 0.11% | 98.03% | NA |
| Indica Intermediate | 786 | 2.70% | 1.90% | 0.51% | 94.91% | NA |
| Temperate Japonica | 767 | 93.20% | 5.90% | 0.78% | 0.13% | NA |
| Tropical Japonica | 504 | 12.90% | 48.80% | 1.19% | 37.10% | NA |
| Japonica Intermediate | 241 | 24.90% | 57.70% | 1.66% | 15.77% | NA |
| VI/Aromatic | 96 | 3.10% | 79.20% | 1.04% | 16.67% | NA |
| Intermediate | 90 | 22.20% | 22.20% | 4.44% | 51.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0317761695 | TGTAGGGTGATCTTAACATAACCA -> T | LOC_Os03g31190.1 | frameshift_variant ; p.Leu117fs; HIGH | frameshift_variant | Average:19.954; most accessible tissue: Minghui63 panicle, score: 42.799 | N | N | N | N |
| vg0317761695 | TGTAGGGTGATCTTAACATAACCA -> DEL | LOC_Os03g31190.1 | N | frameshift_variant | Average:19.954; most accessible tissue: Minghui63 panicle, score: 42.799 | N | N | N | N |