| Variant ID: vg1007912549 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 7912549 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 372. )
TGTACACCTCTGATCAGAGTATAATCTATTCGAATAGCCGCGCCCTCGGTTATGGGCAAGCCGAGCAATGTACCCAAGTTAGTGTTTTAATTCTTAAAAC[C/T]
TGCTTAACAACTAAAATATGGAATGGTTGGCCTGGGTTGGCTTGGGACGAGCTGGGACCCAGGGTCGGGTTGCCAGTTCGGTCTGAATCATCGTAGGCCT
AGGCCTACGATGATTCAGACCGAACTGGCAACCCGACCCTGGGTCCCAGCTCGTCCCAAGCCAACCCAGGCCAACCATTCCATATTTTAGTTGTTAAGCA[G/A]
GTTTTAAGAATTAAAACACTAACTTGGGTACATTGCTCGGCTTGCCCATAACCGAGGGCGCGGCTATTCGAATAGATTATACTCTGATCAGAGGTGTACA
| 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 | 43.90% | 0.50% | 46.06% | 9.48% | NA |
| All Indica | 2759 | 43.90% | 0.20% | 47.05% | 8.81% | NA |
| All Japonica | 1512 | 44.20% | 1.10% | 42.53% | 12.17% | NA |
| Aus | 269 | 51.70% | 0.00% | 45.72% | 2.60% | NA |
| Indica I | 595 | 34.60% | 0.20% | 61.18% | 4.03% | NA |
| Indica II | 465 | 57.00% | 0.20% | 35.91% | 6.88% | NA |
| Indica III | 913 | 40.60% | 0.20% | 45.13% | 14.02% | NA |
| Indica Intermediate | 786 | 47.10% | 0.30% | 45.17% | 7.51% | NA |
| Temperate Japonica | 767 | 58.70% | 0.80% | 33.90% | 6.65% | NA |
| Tropical Japonica | 504 | 15.50% | 1.80% | 61.11% | 21.63% | NA |
| Japonica Intermediate | 241 | 58.10% | 0.80% | 31.12% | 9.96% | NA |
| VI/Aromatic | 96 | 15.60% | 1.00% | 75.00% | 8.33% | NA |
| Intermediate | 90 | 47.80% | 0.00% | 45.56% | 6.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1007912549 | C -> T | LOC_Os10g15100.1 | intron_variant ; MODIFIER | silent_mutation | Average:24.853; most accessible tissue: Zhenshan97 root, score: 47.644 | N | N | N | N |
| vg1007912549 | C -> DEL | N | N | silent_mutation | Average:24.853; most accessible tissue: Zhenshan97 root, score: 47.644 | N | N | N | N |