| Variant ID: vg0409515192 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 9515192 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CGTCAACCCAAACACTTGGGTAATACTTCTTCAAGTATTTGCCATTGAGCGCCCATCCATAAACCTCACCATCAAGCCCTTGCAACATATATGCCCCTTT[A/T]
GACACAACATTATAGATTTGAAACGGTCCTTCCCAATTTGGTGACCACTTGCCGAACTTGTTATCCCGAGTTCCAATCGGCAAAATCAACTTCCATACAA
TTGTATGGAAGTTGATTTTGCCGATTGGAACTCGGGATAACAAGTTCGGCAAGTGGTCACCAAATTGGGAAGGACCGTTTCAAATCTATAATGTTGTGTC[T/A]
AAAGGGGCATATATGTTGCAAGGGCTTGATGGTGAGGTTTATGGATGGGCGCTCAATGGCAAATACTTGAAGAAGTATTACCCAAGTGTTTGGGTTGACG
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 90.80% | 0.10% | 0.28% | 8.87% | NA |
| All Indica | 2759 | 99.90% | 0.00% | 0.04% | 0.04% | NA |
| All Japonica | 1512 | 73.30% | 0.00% | 0.73% | 25.93% | NA |
| Aus | 269 | 99.30% | 0.70% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.80% | 0.00% | 0.00% | 0.22% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.70% | 0.10% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 98.60% | 0.00% | 0.00% | 1.43% | NA |
| Tropical Japonica | 504 | 31.50% | 0.00% | 1.79% | 66.67% | NA |
| Japonica Intermediate | 241 | 80.50% | 0.00% | 0.83% | 18.67% | NA |
| VI/Aromatic | 96 | 72.90% | 0.00% | 1.04% | 26.04% | NA |
| Intermediate | 90 | 98.90% | 0.00% | 0.00% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0409515192 | A -> DEL | LOC_Os04g17380.1 | N | frameshift_variant | Average:35.215; most accessible tissue: Minghui63 young leaf, score: 56.213 | N | N | N | N |
| vg0409515192 | A -> T | LOC_Os04g17380.1 | synonymous_variant ; p.Ser138Ser; LOW | synonymous_codon | Average:35.215; most accessible tissue: Minghui63 young leaf, score: 56.213 | N | N | N | N |