| Variant ID: vg1007912801 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 7912801 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
TAGTACTAGATTCGTGTTTGCAAAATAGCCCTGAGCAACTAAATATCTTTAAACGCTGTTTACTGCAACCCTAACCCTTTATATTATAATTCCTTTGTAC[T/C]
CCCTTGCATTTATTCTGCACTTGTGGGTGTGTCTTGTTGAGTACGGTGGTTGTACTCAGTCTTGCTCAATTTTTCCCAAACCCAGAAGAGGAGTTCCTGG
CCAGGAACTCCTCTTCTGGGTTTGGGAAAAATTGAGCAAGACTGAGTACAACCACCGTACTCAACAAGACACACCCACAAGTGCAGAATAAATGCAAGGG[A/G]
GTACAAAGGAATTATAATATAAAGGGTTAGGGTTGCAGTAAACAGCGTTTAAAGATATTTAGTTGCTCAGGGCTATTTTGCAAACACGAATCTAGTACTA
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 17.80% | 0.20% | 37.45% | 44.54% | NA |
| All Indica | 2759 | 5.80% | 0.30% | 38.31% | 55.60% | NA |
| All Japonica | 1512 | 42.20% | 0.00% | 29.96% | 27.84% | NA |
| Aus | 269 | 4.10% | 0.00% | 60.22% | 35.69% | NA |
| Indica I | 595 | 10.10% | 0.20% | 30.08% | 59.66% | NA |
| Indica II | 465 | 5.80% | 0.20% | 35.91% | 58.06% | NA |
| Indica III | 913 | 3.30% | 0.50% | 46.00% | 50.16% | NA |
| Indica Intermediate | 786 | 5.50% | 0.10% | 37.02% | 57.38% | NA |
| Temperate Japonica | 767 | 58.30% | 0.00% | 25.95% | 15.78% | NA |
| Tropical Japonica | 504 | 11.30% | 0.00% | 44.44% | 44.25% | NA |
| Japonica Intermediate | 241 | 55.60% | 0.00% | 12.45% | 31.95% | NA |
| VI/Aromatic | 96 | 8.30% | 1.00% | 65.62% | 25.00% | NA |
| Intermediate | 90 | 27.80% | 0.00% | 38.89% | 33.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1007912801 | T -> C | LOC_Os10g15100.1 | intron_variant ; MODIFIER | silent_mutation | Average:11.874; most accessible tissue: Zhenshan97 root, score: 18.731 | N | N | N | N |
| vg1007912801 | T -> DEL | N | N | silent_mutation | Average:11.874; most accessible tissue: Zhenshan97 root, score: 18.731 | N | N | N | N |