| Variant ID: vg0206136220 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 6136220 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: G |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, others allele: 0.00, population size: 354. )
TCTCATGAAGTAGTTCAAAGGCATCTTCCACACCTTCCTCGCCAACTGAACCCCCTCCATCCAAATGAGAAGAAACTACATCCCTCTGGAAGGTATAATT[G/T]
TTGTGTTATAGTTACATCAAGTAGATGTTACATCATTGAACTACAGAGCCAACAAAATGCAGAAAAACTTACATTGTACTTCAAAATGTAGAATGAGGTG
CACCTCATTCTACATTTTGAAGTACAATGTAAGTTTTTCTGCATTTTGTTGGCTCTGTAGTTCAATGATGTAACATCTACTTGATGTAACTATAACACAA[C/A]
AATTATACCTTCCAGAGGGATGTAGTTTCTTCTCATTTGGATGGAGGGGGTTCAGTTGGCGAGGAAGGTGTGGAAGATGCCTTTGAACTACTTCATGAGA
| Populations | Population Size | Frequency of T(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 69.30% | 30.70% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 8.30% | 91.70% | 0.00% | 0.00% | NA |
| Aus | 269 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.40% | 0.60% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 11.20% | 88.80% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 4.80% | 95.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 6.20% | 93.80% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 80.20% | 19.80% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 62.20% | 37.80% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0206136220 | G -> T | LOC_Os02g11840.1 | intron_variant ; MODIFIER | silent_mutation | Average:37.991; most accessible tissue: Minghui63 root, score: 55.188 | N | N | N | N |
| vg0206136220 | G -> T | LOC_Os02g11840.2 | intron_variant ; MODIFIER | silent_mutation | Average:37.991; most accessible tissue: Minghui63 root, score: 55.188 | N | N | N | N |