| Variant ID: vg0605309577 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr06 | Position: 5309577 |
| Reference Allele: ATAG | Alternative Allele: A |
| Primary Allele: ATAG | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CATCAGGAGACAGGATTTTGAAAAAGGGGGGGGGGGGGAAGGTGATTGATTGGCTCGTTGAATTTTTGATGATTTTTATAATGTCTATTTCATAGTATTA[ATAG/A]
TAGTATGCACAAGAAATAAACGTGCTGATTCAGTCAAAGATTTTTTTAGAAAATAGTATACCTGGAGTAACTTCACGATGTCGCCTCATGATATATTGGA
TCCAATATATCATGAGGCGACATCGTGAAGTTACTCCAGGTATACTATTTTCTAAAAAAATCTTTGACTGAATCAGCACGTTTATTTCTTGTGCATACTA[CTAT/T]
TAATACTATGAAATAGACATTATAAAAATCATCAAAAATTCAACGAGCCAATCAATCACCTTCCCCCCCCCCCCCTTTTTCAAAATCCTGTCTCCTGATG
| Populations | Population Size | Frequency of ATAG(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 86.80% | 10.90% | 1.88% | 0.36% | NA |
| All Indica | 2759 | 79.50% | 18.00% | 2.07% | 0.43% | NA |
| All Japonica | 1512 | 99.40% | 0.50% | 0.13% | 0.00% | NA |
| Aus | 269 | 88.10% | 0.40% | 10.04% | 1.49% | NA |
| Indica I | 595 | 65.90% | 33.80% | 0.34% | 0.00% | NA |
| Indica II | 465 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica III | 913 | 74.70% | 20.00% | 4.27% | 0.99% | NA |
| Indica Intermediate | 786 | 83.50% | 14.10% | 2.04% | 0.38% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 98.40% | 1.20% | 0.40% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 96.90% | 3.10% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 86.70% | 8.90% | 3.33% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0605309577 | ATAG -> A | LOC_Os06g10320.1 | downstream_gene_variant ; 2847.0bp to feature; MODIFIER | silent_mutation | Average:69.278; most accessible tissue: Minghui63 young leaf, score: 82.907 | N | N | N | N |
| vg0605309577 | ATAG -> A | LOC_Os06g10330.1 | downstream_gene_variant ; 1831.0bp to feature; MODIFIER | silent_mutation | Average:69.278; most accessible tissue: Minghui63 young leaf, score: 82.907 | N | N | N | N |
| vg0605309577 | ATAG -> A | LOC_Os06g10340.1 | intron_variant ; MODIFIER | silent_mutation | Average:69.278; most accessible tissue: Minghui63 young leaf, score: 82.907 | N | N | N | N |
| vg0605309577 | ATAG -> DEL | N | N | silent_mutation | Average:69.278; most accessible tissue: Minghui63 young leaf, score: 82.907 | N | N | N | N |