| Variant ID: vg0605309496 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr06 | Position: 5309496 |
| Reference Allele: GAA | Alternative Allele: G |
| Primary Allele: GAA | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
ATTTGGGGGGACTATGTTGTAATACCCTAGAAAAATGTTGTTAGGTGAGGCATCCTGCAGCAACGTGGCCTTCATTGTATCCATCAGGAGACAGGATTTT[GAA/G]
AAAGGGGGGGGGGGGGAAGGTGATTGATTGGCTCGTTGAATTTTTGATGATTTTTATAATGTCTATTTCATAGTATTAATAGTAGTATGCACAAGAAATA
TATTTCTTGTGCATACTACTATTAATACTATGAAATAGACATTATAAAAATCATCAAAAATTCAACGAGCCAATCAATCACCTTCCCCCCCCCCCCCTTT[TTC/C]
AAAATCCTGTCTCCTGATGGATACAATGAAGGCCACGTTGCTGCAGGATGCCTCACCTAACAACATTTTTCTAGGGTATTACAACATAGTCCCCCCAAAT
| Populations | Population Size | Frequency of GAA(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 89.00% | 1.50% | 9.42% | 0.08% | NA |
| All Indica | 2759 | 82.40% | 2.20% | 15.33% | 0.11% | NA |
| All Japonica | 1512 | 99.90% | 0.00% | 0.07% | 0.00% | NA |
| Aus | 269 | 89.60% | 3.70% | 6.32% | 0.37% | NA |
| Indica I | 595 | 71.30% | 0.00% | 28.74% | 0.00% | NA |
| Indica II | 465 | 99.10% | 0.00% | 0.43% | 0.43% | NA |
| Indica III | 913 | 78.10% | 4.60% | 17.31% | 0.00% | NA |
| Indica Intermediate | 786 | 85.90% | 2.30% | 11.70% | 0.13% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.00% | 0.20% | 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% | 2.20% | 4.44% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0605309496 | GAA -> G | LOC_Os06g10320.1 | downstream_gene_variant ; 2766.0bp to feature; MODIFIER | silent_mutation | Average:75.243; most accessible tissue: Minghui63 young leaf, score: 85.028 | N | N | N | N |
| vg0605309496 | GAA -> G | LOC_Os06g10330.1 | downstream_gene_variant ; 1750.0bp to feature; MODIFIER | silent_mutation | Average:75.243; most accessible tissue: Minghui63 young leaf, score: 85.028 | N | N | N | N |
| vg0605309496 | GAA -> G | LOC_Os06g10340.1 | intron_variant ; MODIFIER | silent_mutation | Average:75.243; most accessible tissue: Minghui63 young leaf, score: 85.028 | N | N | N | N |
| vg0605309496 | GAA -> DEL | N | N | silent_mutation | Average:75.243; most accessible tissue: Minghui63 young leaf, score: 85.028 | N | N | N | N |