| Variant ID: vg0424199561 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 24199561 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CTCTTTATCAGCTCTTCCTCAACGGGTACACAGAGATGGTCCGTTGCCTACACAAATATAGCATTTTAGTGATTAACAAAAAAAAAGTTGAAAGAAGAGA[C/T]
AACGATGAATATCCGTACACTACCTATGGTTATAAATAAGCTTTCTGTTAGATAAGTTTTAGAAAAAATCTACTAATAAATTTATATGATATTATGATAG
CTATCATAATATCATATAAATTTATTAGTAGATTTTTTCTAAAACTTATCTAACAGAAAGCTTATTTATAACCATAGGTAGTGTACGGATATTCATCGTT[G/A]
TCTCTTCTTTCAACTTTTTTTTTGTTAATCACTAAAATGCTATATTTGTGTAGGCAACGGACCATCTCTGTGTACCCGTTGAGGAAGAGCTGATAAAGAG
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 98.50% | 0.20% | 0.17% | 1.16% | NA |
| All Indica | 2759 | 98.20% | 0.40% | 0.18% | 1.30% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 92.20% | 0.00% | 1.12% | 6.69% | NA |
| Indica I | 595 | 99.80% | 0.00% | 0.00% | 0.17% | NA |
| Indica II | 465 | 99.40% | 0.60% | 0.00% | 0.00% | NA |
| Indica III | 913 | 96.40% | 0.10% | 0.44% | 3.07% | NA |
| Indica Intermediate | 786 | 98.20% | 0.80% | 0.13% | 0.89% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0424199561 | C -> DEL | N | N | silent_mutation | Average:33.32; most accessible tissue: Callus, score: 76.576 | N | N | N | N |
| vg0424199561 | C -> T | LOC_Os04g40770.1 | downstream_gene_variant ; 4211.0bp to feature; MODIFIER | silent_mutation | Average:33.32; most accessible tissue: Callus, score: 76.576 | N | N | N | N |
| vg0424199561 | C -> T | LOC_Os04g40790.1 | downstream_gene_variant ; 2752.0bp to feature; MODIFIER | silent_mutation | Average:33.32; most accessible tissue: Callus, score: 76.576 | N | N | N | N |
| vg0424199561 | C -> T | LOC_Os04g40780.1 | intron_variant ; MODIFIER | silent_mutation | Average:33.32; most accessible tissue: Callus, score: 76.576 | N | N | N | N |