| Variant ID: vg0918112154 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr09 | Position: 18112154 |
| Reference Allele: A | Alternative Allele: AT |
| Primary Allele: AT | Secondary Allele: A |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 318. )
GAAAGCATATCACTTCATTTGTGACAGTGTGAGATACCTTCACAGTGTTAGGATATGCTATGTAGTCCTATATTTGCAAATAACCAACAAGCAGAGAAAC[A/AT]
TTTTTTTCCCTCCGAAAAATTGTGCCAAAACTCATGTATATCACTTATTTTTCCTTCCAAATGTGCTGTTTCTCACCAACATATGGAGAATTCTGAAATC
GATTTCAGAATTCTCCATATGTTGGTGAGAAACAGCACATTTGGAAGGAAAAATAAGTGATATACATGAGTTTTGGCACAATTTTTCGGAGGGAAAAAAA[T/AT]
GTTTCTCTGCTTGTTGGTTATTTGCAAATATAGGACTACATAGCATATCCTAACACTGTGAAGGTATCTCACACTGTCACAAATGAAGTGATATGCTTTC
| Populations | Population Size | Frequency of AT(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 66.30% | 33.50% | 0.13% | 0.06% | NA |
| All Indica | 2759 | 95.90% | 3.90% | 0.14% | 0.11% | NA |
| All Japonica | 1512 | 7.70% | 92.30% | 0.07% | 0.00% | NA |
| Aus | 269 | 94.10% | 5.90% | 0.00% | 0.00% | NA |
| Indica I | 595 | 92.40% | 7.20% | 0.17% | 0.17% | NA |
| Indica II | 465 | 96.60% | 3.20% | 0.22% | 0.00% | NA |
| Indica III | 913 | 97.70% | 2.10% | 0.11% | 0.11% | NA |
| Indica Intermediate | 786 | 95.90% | 3.80% | 0.13% | 0.13% | NA |
| Temperate Japonica | 767 | 14.30% | 85.50% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 0.60% | 99.40% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 1.20% | 98.80% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 80.20% | 19.80% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 48.90% | 50.00% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0918112154 | A -> DEL | N | N | silent_mutation | Average:55.456; most accessible tissue: Zhenshan97 panicle, score: 72.468 | N | N | N | N |
| vg0918112154 | A -> AT | LOC_Os09g29790.1 | upstream_gene_variant ; 2842.0bp to feature; MODIFIER | silent_mutation | Average:55.456; most accessible tissue: Zhenshan97 panicle, score: 72.468 | N | N | N | N |
| vg0918112154 | A -> AT | LOC_Os09g29810.1 | upstream_gene_variant ; 2970.0bp to feature; MODIFIER | silent_mutation | Average:55.456; most accessible tissue: Zhenshan97 panicle, score: 72.468 | N | N | N | N |
| vg0918112154 | A -> AT | LOC_Os09g29800.1 | intron_variant ; MODIFIER | silent_mutation | Average:55.456; most accessible tissue: Zhenshan97 panicle, score: 72.468 | N | N | N | N |