| Variant ID: vg1007912486 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 7912486 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 418. )
GTATACCGTGGTGGTATGTGGCACGTGGTTACACGTGAGGAAGATGTGTCTTGTGGGTAAAGATGTACACCTCTGATCAGAGTATAATCTATTCGAATAG[C/T]
CGCGCCCTCGGTTATGGGCAAGCCGAGCAATGTACCCAAGTTAGTGTTTTAATTCTTAAAACCTGCTTAACAACTAAAATATGGAATGGTTGGCCTGGGT
ACCCAGGCCAACCATTCCATATTTTAGTTGTTAAGCAGGTTTTAAGAATTAAAACACTAACTTGGGTACATTGCTCGGCTTGCCCATAACCGAGGGCGCG[G/A]
CTATTCGAATAGATTATACTCTGATCAGAGGTGTACATCTTTACCCACAAGACACATCTTCCTCACGTGTAACCACGTGCCACATACCACCACGGTATAC
| 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 | 12.40% | 0.10% | 46.64% | 40.86% | NA |
| All Indica | 2759 | 16.60% | 0.00% | 45.81% | 37.55% | NA |
| All Japonica | 1512 | 5.70% | 0.30% | 44.71% | 49.34% | NA |
| Aus | 269 | 10.00% | 0.00% | 59.85% | 30.11% | NA |
| Indica I | 595 | 25.70% | 0.00% | 49.58% | 24.71% | NA |
| Indica II | 465 | 11.40% | 0.00% | 42.58% | 46.02% | NA |
| Indica III | 913 | 11.50% | 0.00% | 47.86% | 40.64% | NA |
| Indica Intermediate | 786 | 18.70% | 0.10% | 42.49% | 38.68% | NA |
| Temperate Japonica | 767 | 3.00% | 0.00% | 50.07% | 46.94% | NA |
| Tropical Japonica | 504 | 5.00% | 0.60% | 39.68% | 54.76% | NA |
| Japonica Intermediate | 241 | 15.80% | 0.40% | 38.17% | 45.64% | NA |
| VI/Aromatic | 96 | 8.30% | 1.00% | 60.42% | 30.21% | NA |
| Intermediate | 90 | 6.70% | 0.00% | 50.00% | 43.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1007912486 | C -> T | LOC_Os10g15100.1 | intron_variant ; MODIFIER | silent_mutation | Average:24.931; most accessible tissue: Zhenshan97 flag leaf, score: 48.165 | N | N | N | N |
| vg1007912486 | C -> DEL | N | N | silent_mutation | Average:24.931; most accessible tissue: Zhenshan97 flag leaf, score: 48.165 | N | N | N | N |