| Variant ID: vg0409515204 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr04 | Position: 9515204 |
| Reference Allele: A | Alternative Allele: ATTT,T |
| Primary Allele: A | Secondary Allele: ATTT |
Inferred Ancestral Allele: Not determined.
CACTTGGGTAATACTTCTTCAAGTATTTGCCATTGAGCGCCCATCCATAAACCTCACCATCAAGCCCTTGCAACATATATGCCCCTTTAGACACAACATT[A/ATTT,T]
TAGATTTGAAACGGTCCTTCCCAATTTGGTGACCACTTGCCGAACTTGTTATCCCGAGTTCCAATCGGCAAAATCAACTTCCATACAAGTTCACCTTCCG
CGGAAGGTGAACTTGTATGGAAGTTGATTTTGCCGATTGGAACTCGGGATAACAAGTTCGGCAAGTGGTCACCAAATTGGGAAGGACCGTTTCAAATCTA[T/AAAT,A]
AATGTTGTGTCTAAAGGGGCATATATGTTGCAAGGGCTTGATGGTGAGGTTTATGGATGGGCGCTCAATGGCAAATACTTGAAGAAGTATTACCCAAGTG
| Populations | Population Size | Frequency of A(primary allele) | Frequency of ATTT(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 90.20% | 0.40% | 0.49% | 8.87% | T: 0.13% |
| All Indica | 2759 | 99.10% | 0.50% | 0.29% | 0.00% | T: 0.11% |
| All Japonica | 1512 | 73.30% | 0.10% | 0.66% | 25.99% | NA |
| Aus | 269 | 98.10% | 0.40% | 0.74% | 0.00% | T: 0.74% |
| Indica I | 595 | 99.30% | 0.20% | 0.50% | 0.00% | NA |
| Indica II | 465 | 98.70% | 0.60% | 0.65% | 0.00% | NA |
| Indica III | 913 | 98.90% | 0.80% | 0.11% | 0.00% | T: 0.22% |
| Indica Intermediate | 786 | 99.40% | 0.40% | 0.13% | 0.00% | T: 0.13% |
| Temperate Japonica | 767 | 98.60% | 0.00% | 0.00% | 1.43% | NA |
| Tropical Japonica | 504 | 31.30% | 0.20% | 1.59% | 66.87% | NA |
| Japonica Intermediate | 241 | 80.50% | 0.00% | 0.83% | 18.67% | NA |
| VI/Aromatic | 96 | 70.80% | 1.00% | 2.08% | 26.04% | NA |
| Intermediate | 90 | 96.70% | 0.00% | 1.11% | 1.11% | T: 1.11% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0409515204 | A -> DEL | LOC_Os04g17380.1 | N | frameshift_variant | Average:35.917; most accessible tissue: Minghui63 young leaf, score: 56.213 | N | N | N | N |
| vg0409515204 | A -> ATTT | LOC_Os04g17380.1 | stop_gained&disruptive_inframe_insertion ; p.Tyr134delinsTerAsn; HIGH | inframe_variant | Average:35.917; most accessible tissue: Minghui63 young leaf, score: 56.213 | N | N | N | N |
| vg0409515204 | A -> T | LOC_Os04g17380.1 | stop_gained ; p.Tyr134*; HIGH | stop_gained | Average:35.917; most accessible tissue: Minghui63 young leaf, score: 56.213 | N | N | N | N |