| Variant ID: vg1007912745 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 7912745 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
GGCCTTGGGTTAAGGCAGGTTCGTGTGGGTTCACGGCCTTGATAATTAACATTGTATAGTACTAGATTCGTGTTTGCAAAATAGCCCTGAGCAACTAAAT[A/G]
TCTTTAAACGCTGTTTACTGCAACCCTAACCCTTTATATTATAATTCCTTTGTACTCCCTTGCATTTATTCTGCACTTGTGGGTGTGTCTTGTTGAGTAC
GTACTCAACAAGACACACCCACAAGTGCAGAATAAATGCAAGGGAGTACAAAGGAATTATAATATAAAGGGTTAGGGTTGCAGTAAACAGCGTTTAAAGA[T/C]
ATTTAGTTGCTCAGGGCTATTTTGCAAACACGAATCTAGTACTATACAATGTTAATTATCAAGGCCGTGAACCCACACGAACCTGCCTTAACCCAAGGCC
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 15.50% | 0.10% | 5.42% | 78.95% | NA |
| All Indica | 2759 | 3.70% | 0.10% | 1.38% | 94.85% | NA |
| All Japonica | 1512 | 40.10% | 0.10% | 9.85% | 50.00% | NA |
| Aus | 269 | 1.50% | 0.00% | 7.06% | 91.45% | NA |
| Indica I | 595 | 6.70% | 0.00% | 0.50% | 92.77% | NA |
| Indica II | 465 | 4.70% | 0.00% | 1.29% | 93.98% | NA |
| Indica III | 913 | 1.30% | 0.10% | 1.53% | 97.04% | NA |
| Indica Intermediate | 786 | 3.60% | 0.10% | 1.91% | 94.40% | NA |
| Temperate Japonica | 767 | 56.50% | 0.00% | 15.78% | 27.77% | NA |
| Tropical Japonica | 504 | 8.30% | 0.20% | 3.57% | 87.90% | NA |
| Japonica Intermediate | 241 | 54.40% | 0.00% | 4.15% | 41.49% | NA |
| VI/Aromatic | 96 | 3.10% | 2.10% | 43.75% | 51.04% | NA |
| Intermediate | 90 | 21.10% | 0.00% | 8.89% | 70.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1007912745 | A -> G | LOC_Os10g15100.1 | intron_variant ; MODIFIER | silent_mutation | Average:16.787; most accessible tissue: Zhenshan97 root, score: 29.203 | N | N | N | N |
| vg1007912745 | A -> DEL | N | N | silent_mutation | Average:16.787; most accessible tissue: Zhenshan97 root, score: 29.203 | N | N | N | N |