| Variant ID: vg0324793542 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr03 | Position: 24793542 |
| Reference Allele: T | Alternative Allele: TA |
| Primary Allele: T | Secondary Allele: TA |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 259. )
GGCGAGTTCTCCCTTCAGCATAACGACCTGCACAATTATATTCTCCTCACGATCAGCATAACTTGCCTAAAACATTTCAACAAAACAAACAAACCACTGA[T/TA]
AAAAAAAATATAAAGCTCACCATCATAAAGTGGAGCTAAATCATCAAAATATGGGAACGACTTATCTCGCCAATGAATTGCATCTTTGTTCTTGCGATCA
TGATCGCAAGAACAAAGATGCAATTCATTGGCGAGATAAGTCGTTCCCATATTTTGATGATTTAGCTCCACTTTATGATGGTGAGCTTTATATTTTTTTT[A/TA]
TCAGTGGTTTGTTTGTTTTGTTGAAATGTTTTAGGCAAGTTATGCTGATCGTGAGGAGAATATAATTGTGCAGGTCGTTATGCTGAAGGGAGAACTCGCC
| Populations | Population Size | Frequency of T(primary allele) | Frequency of TA(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 52.70% | 0.30% | 12.76% | 34.21% | NA |
| All Indica | 2759 | 28.90% | 0.50% | 16.75% | 53.90% | NA |
| All Japonica | 1512 | 99.30% | 0.10% | 0.07% | 0.60% | NA |
| Aus | 269 | 18.60% | 0.00% | 47.96% | 33.46% | NA |
| Indica I | 595 | 59.50% | 1.30% | 16.30% | 22.86% | NA |
| Indica II | 465 | 8.40% | 0.00% | 3.44% | 88.17% | NA |
| Indica III | 913 | 13.60% | 0.10% | 24.86% | 61.45% | NA |
| Indica Intermediate | 786 | 35.60% | 0.50% | 15.52% | 48.35% | NA |
| Temperate Japonica | 767 | 99.20% | 0.10% | 0.13% | 0.52% | NA |
| Tropical Japonica | 504 | 99.20% | 0.00% | 0.00% | 0.79% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 90.60% | 0.00% | 4.17% | 5.21% | NA |
| Intermediate | 90 | 62.20% | 1.10% | 7.78% | 28.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0324793542 | T -> TA | LOC_Os03g44140.1 | downstream_gene_variant ; 4261.0bp to feature; MODIFIER | silent_mutation | Average:4.687; most accessible tissue: Zhenshan97 flower, score: 9.663 | N | N | N | N |
| vg0324793542 | T -> TA | LOC_Os03g44130.1 | intron_variant ; MODIFIER | silent_mutation | Average:4.687; most accessible tissue: Zhenshan97 flower, score: 9.663 | N | N | N | N |
| vg0324793542 | T -> DEL | N | N | silent_mutation | Average:4.687; most accessible tissue: Zhenshan97 flower, score: 9.663 | N | N | N | N |