| Variant ID: vg0128509437 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 28509437 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
GTGCCGTTGTACGGCGGTGCCAGATTGGGGTGTGACATATATGAACGATGGGAGGCGCGTGATGGTGGCGGTGTCTAGGCCGAACCTGGGCAGCGTCGGC[T/C]
GCTGCTGCTCCTGCTCCATGACCAGTGGACGATCACGCCGGCGACAGGCAATGCGGAGGGCTCGAGGGCAGATGAAGATGGTGATGAGGAAGAAGCTTAG
CTAAGCTTCTTCCTCATCACCATCTTCATCTGCCCTCGAGCCCTCCGCATTGCCTGTCGCCGGCGTGATCGTCCACTGGTCATGGAGCAGGAGCAGCAGC[A/G]
GCCGACGCTGCCCAGGTTCGGCCTAGACACCGCCACCATCACGCGCCTCCCATCGTTCATATATGTCACACCCCAATCTGGCACCGCCGTACAACGGCAC
| 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 | 25.10% | 9.90% | 9.50% | 55.46% | NA |
| All Indica | 2759 | 1.60% | 12.40% | 13.56% | 72.45% | NA |
| All Japonica | 1512 | 72.20% | 7.70% | 4.03% | 16.14% | NA |
| Aus | 269 | 4.10% | 0.40% | 1.12% | 94.42% | NA |
| Indica I | 595 | 1.80% | 4.90% | 6.55% | 86.72% | NA |
| Indica II | 465 | 2.60% | 9.50% | 5.38% | 82.58% | NA |
| Indica III | 913 | 0.50% | 21.40% | 27.71% | 50.38% | NA |
| Indica Intermediate | 786 | 1.90% | 9.50% | 7.25% | 81.30% | NA |
| Temperate Japonica | 767 | 92.70% | 0.00% | 0.13% | 7.17% | NA |
| Tropical Japonica | 504 | 33.10% | 21.60% | 10.91% | 34.33% | NA |
| Japonica Intermediate | 241 | 88.40% | 2.90% | 2.07% | 6.64% | NA |
| VI/Aromatic | 96 | 13.50% | 0.00% | 2.08% | 84.38% | NA |
| Intermediate | 90 | 31.10% | 11.10% | 10.00% | 47.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0128509437 | T -> DEL | LOC_Os01g49570.1 | N | frameshift_variant | Average:24.383; most accessible tissue: Callus, score: 48.491 | N | N | N | N |
| vg0128509437 | T -> C | LOC_Os01g49570.1 | missense_variant ; p.Gln46Arg; MODERATE | nonsynonymous_codon ; Q46R | Average:24.383; most accessible tissue: Callus, score: 48.491 | unknown | unknown | TOLERATED | 0.92 |