| Variant ID: vg0409081713 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 9081713 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GTTCTTATGCATAAGGATAACTCATCCTAAGAACATCTATTAGGACTACTCCCATAGTATATAATGCCCACTTTAGAGGTCTAAGATCCTCCCCTGCGAC[T/A]
ACATTAATTGTAGGTGCCCTAAGATTCACATACCAGAGGGGCTTCCCATACTTTTTTTAAGGTAAAACAAAGGCCAGTGTATTGAAAACTGGGATGGTTG
CAACCATCCCAGTTTTCAATACACTGGCCTTTGTTTTACCTTAAAAAAAGTATGGGAAGCCCCTCTGGTATGTGAATCTTAGGGCACCTACAATTAATGT[A/T]
GTCGCAGGGGAGGATCTTAGACCTCTAAAGTGGGCATTATATACTATGGGAGTAGTCCTAATAGATGTTCTTAGGATGAGTTATCCTTATGCATAAGAAC
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 97.20% | 2.80% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 96.80% | 3.20% | 0.00% | 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 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 92.70% | 7.30% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 96.30% | 3.70% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 24.00% | 76.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 91.10% | 8.90% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0409081713 | T -> A | LOC_Os04g16680.1 | upstream_gene_variant ; 3825.0bp to feature; MODIFIER | silent_mutation | Average:58.935; most accessible tissue: Minghui63 flag leaf, score: 79.962 | N | N | N | N |
| vg0409081713 | T -> A | LOC_Os04g16700.1 | downstream_gene_variant ; 3351.0bp to feature; MODIFIER | silent_mutation | Average:58.935; most accessible tissue: Minghui63 flag leaf, score: 79.962 | N | N | N | N |
| vg0409081713 | T -> A | LOC_Os04g16690.1 | intron_variant ; MODIFIER | silent_mutation | Average:58.935; most accessible tissue: Minghui63 flag leaf, score: 79.962 | N | N | N | N |