| Variant ID: vg0317761795 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr03 | Position: 17761795 |
| Reference Allele: TAGAACAGGAACA | Alternative Allele: T |
| Primary Allele: TAGAACAGGAACA | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TGTAGGGTGATCTTAACATAACCAGTAGCATACTATGCGCATCATGAATGTCAAGAACAGGAACATACCAGTAACACGATAACATGCTAGAGGCATCATG[TAGAACAGGAACA/T]
AGAACAGGAACAAGAATATAGCGCACATAGTATAGCGCTAACAATGGGAACAGGAATAGCGCTAACAGCAGTAGCAGGAGGAGAAGATTATACCCCGAGA
TCTCGGGGTATAATCTTCTCCTCCTGCTACTGCTGTTAGCGCTATTCCTGTTCCCATTGTTAGCGCTATACTATGTGCGCTATATTCTTGTTCCTGTTCT[TGTTCCTGTTCTA/A]
CATGATGCCTCTAGCATGTTATCGTGTTACTGGTATGTTCCTGTTCTTGACATTCATGATGCGCATAGTATGCTACTGGTTATGTTAAGATCACCCTACA
| Populations | Population Size | Frequency of TAGAACAGGAACA(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 32.20% | 0.20% | 4.13% | 63.46% | NA |
| All Indica | 2759 | 3.90% | 0.00% | 5.76% | 90.36% | NA |
| All Japonica | 1512 | 84.90% | 0.50% | 0.46% | 14.15% | NA |
| Aus | 269 | 1.90% | 0.00% | 7.43% | 90.71% | NA |
| Indica I | 595 | 4.20% | 0.00% | 9.08% | 86.72% | NA |
| Indica II | 465 | 4.10% | 0.00% | 3.23% | 92.69% | NA |
| Indica III | 913 | 3.00% | 0.00% | 4.38% | 92.66% | NA |
| Indica Intermediate | 786 | 4.60% | 0.00% | 6.36% | 89.06% | NA |
| Temperate Japonica | 767 | 99.90% | 0.00% | 0.00% | 0.13% | NA |
| Tropical Japonica | 504 | 63.10% | 0.60% | 0.99% | 35.32% | NA |
| Japonica Intermediate | 241 | 83.00% | 1.70% | 0.83% | 14.52% | NA |
| VI/Aromatic | 96 | 88.50% | 0.00% | 3.12% | 8.33% | NA |
| Intermediate | 90 | 47.80% | 1.10% | 6.67% | 44.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0317761795 | TAGAACAGGAACA -> T | LOC_Os03g31190.1 | disruptive_inframe_deletion ; p.Val88_Leu91del; MODERATE | inframe_variant | Average:14.587; most accessible tissue: Minghui63 panicle, score: 29.741 | N | N | N | N |
| vg0317761795 | TAGAACAGGAACA -> DEL | LOC_Os03g31190.1 | N | frameshift_variant | Average:14.587; most accessible tissue: Minghui63 panicle, score: 29.741 | N | N | N | N |