| Variant ID: vg0409081591 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr04 | Position: 9081591 |
| Reference Allele: A | Alternative Allele: AT |
| Primary Allele: A | Secondary Allele: AT |
Inferred Ancestral Allele: Not determined.
CTGCAACAGCGGCTGCGACAGCACTCACCGACAGATCTGGTGGGCATCATCACAAGGGTCTTATCTTCTTCGAGAGATAGCATGAGAGGGAATTGTGATT[A/AT]
TTTTTTTATTTCTTATGGATGGTTCTTATGCATAAGGATAACTCATCCTAAGAACATCTATTAGGACTACTCCCATAGTATATAATGCCCACTTTAGAGG
CCTCTAAAGTGGGCATTATATACTATGGGAGTAGTCCTAATAGATGTTCTTAGGATGAGTTATCCTTATGCATAAGAACCATCCATAAGAAATAAAAAAA[T/AT]
AATCACAATTCCCTCTCATGCTATCTCTCGAAGAAGATAAGACCCTTGTGATGATGCCCACCAGATCTGTCGGTGAGTGCTGTCGCAGCCGCTGTTGCAG
| Populations | Population Size | Frequency of A(primary allele) | Frequency of AT(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 88.20% | 11.70% | 0.17% | 0.00% | NA |
| All Indica | 2759 | 99.60% | 0.40% | 0.07% | 0.00% | NA |
| All Japonica | 1512 | 65.30% | 34.50% | 0.26% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 98.70% | 1.10% | 0.22% | 0.00% | NA |
| Indica III | 913 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.50% | 0.40% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 96.60% | 3.40% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 13.30% | 86.10% | 0.60% | 0.00% | NA |
| Japonica Intermediate | 241 | 74.30% | 25.30% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 93.80% | 6.20% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 82.20% | 15.60% | 2.22% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0409081591 | A -> AT | LOC_Os04g16680.1 | upstream_gene_variant ; 3704.0bp to feature; MODIFIER | silent_mutation | Average:65.058; most accessible tissue: Minghui63 flag leaf, score: 82.75 | N | N | N | N |
| vg0409081591 | A -> AT | LOC_Os04g16700.1 | downstream_gene_variant ; 3472.0bp to feature; MODIFIER | silent_mutation | Average:65.058; most accessible tissue: Minghui63 flag leaf, score: 82.75 | N | N | N | N |
| vg0409081591 | A -> AT | LOC_Os04g16690.1 | intron_variant ; MODIFIER | silent_mutation | Average:65.058; most accessible tissue: Minghui63 flag leaf, score: 82.75 | N | N | N | N |