| Variant ID: vg1100142045 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr11 | Position: 142045 |
| Reference Allele: GAA | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: GAA |
Inferred Ancestral Allele : GAA (evidence from allele frequency in Oryza rufipogon: GAA: 0.98, G: 0.02, others allele: 0.00, population size: 241. )
CTATTGCAGCTTTATATAAATTGATAATGTTACCAACAAACAAATATAATAGGATTGCCACATATATAACCAAGATGGGCACTCCCTGTTGAAAATAAAT[GAA/G]
TAACATATTGCGTGCAAAACATAGATTAATTTTGTTTATGTTAGGCAATATTTTGTCATTCTTTCTTCCTTTGGTAGCAAAGTCAGGCATTTACCTAGTC
GACTAGGTAAATGCCTGACTTTGCTACCAAAGGAAGAAAGAATGACAAAATATTGCCTAACATAAACAAAATTAATCTATGTTTTGCACGCAATATGTTA[TTC/C]
ATTTATTTTCAACAGGGAGTGCCCATCTTGGTTATATATGTGGCAATCCTATTATATTTGTTTGTTGGTAACATTATCAATTTATATAAAGCTGCAATAG
| Populations | Population Size | Frequency of G(primary allele) | Frequency of GAA(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 52.10% | 47.50% | 0.28% | 0.08% | NA |
| All Indica | 2759 | 84.80% | 14.70% | 0.43% | 0.11% | NA |
| All Japonica | 1512 | 1.50% | 98.50% | 0.00% | 0.00% | NA |
| Aus | 269 | 27.50% | 72.50% | 0.00% | 0.00% | NA |
| Indica I | 595 | 97.80% | 1.80% | 0.34% | 0.00% | NA |
| Indica II | 465 | 53.50% | 45.80% | 0.65% | 0.00% | NA |
| Indica III | 913 | 92.30% | 7.30% | 0.22% | 0.11% | NA |
| Indica Intermediate | 786 | 84.60% | 14.50% | 0.64% | 0.25% | NA |
| Temperate Japonica | 767 | 1.30% | 98.70% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 1.40% | 98.60% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 2.10% | 97.90% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 9.40% | 90.60% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 22.20% | 75.60% | 1.11% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1100142045 | GAA -> DEL | N | N | silent_mutation | Average:40.384; most accessible tissue: Callus, score: 62.452 | N | N | N | N |
| vg1100142045 | GAA -> G | LOC_Os11g01250.1 | upstream_gene_variant ; 1728.0bp to feature; MODIFIER | silent_mutation | Average:40.384; most accessible tissue: Callus, score: 62.452 | N | N | N | N |
| vg1100142045 | GAA -> G | LOC_Os11g01240.1 | downstream_gene_variant ; 3087.0bp to feature; MODIFIER | silent_mutation | Average:40.384; most accessible tissue: Callus, score: 62.452 | N | N | N | N |
| vg1100142045 | GAA -> G | LOC_Os11g01270.1 | downstream_gene_variant ; 2119.0bp to feature; MODIFIER | silent_mutation | Average:40.384; most accessible tissue: Callus, score: 62.452 | N | N | N | N |
| vg1100142045 | GAA -> G | LOC_Os11g01260.1 | intron_variant ; MODIFIER | silent_mutation | Average:40.384; most accessible tissue: Callus, score: 62.452 | N | N | N | N |