| Variant ID: vg0800071670 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr08 | Position: 71670 |
| Reference Allele: AAG | Alternative Allele: A |
| Primary Allele: AAG | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
ACTAGTAGTTCTAGTACTAGAAGATCACCACCACCAGAATCAATCGATACTGCTGCTCCCACTAGCATACTAGCAATGTGATGGATCCGCCATTTACAAA[AAG/A]
AGAAGGAATTATCCATCCATCCATCCATTGGACCGGTGGCCTAGATGTCGTCGTCTAGCTCGTTCTTCTCTTCCTCTGCACCATCTTCATCTTCTTGGTC
GACCAAGAAGATGAAGATGGTGCAGAGGAAGAGAAGAACGAGCTAGACGACGACATCTAGGCCACCGGTCCAATGGATGGATGGATGGATAATTCCTTCT[CTT/T]
TTTGTAAATGGCGGATCCATCACATTGCTAGTATGCTAGTGGGAGCAGCAGTATCGATTGATTCTGGTGGTGGTGATCTTCTAGTACTAGAACTACTAGT
| Populations | Population Size | Frequency of AAG(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 94.50% | 5.40% | 0.06% | 0.00% | NA |
| All Indica | 2759 | 90.90% | 9.00% | 0.11% | 0.00% | NA |
| All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 95.60% | 4.20% | 0.17% | 0.00% | NA |
| Indica II | 465 | 94.40% | 5.60% | 0.00% | 0.00% | NA |
| Indica III | 913 | 86.10% | 13.90% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 90.70% | 9.00% | 0.25% | 0.00% | NA |
| Temperate Japonica | 767 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 93.30% | 6.70% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0800071670 | AAG -> A | LOC_Os08g01100.1 | 3_prime_UTR_variant ; 41.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0800071670 | AAG -> A | LOC_Os08g01090.1 | upstream_gene_variant ; 4032.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0800071670 | AAG -> A | LOC_Os08g01090.2 | upstream_gene_variant ; 3832.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |