| Variant ID: vg1105974373 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 5974373 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TGCCGAAATCTTTTTTCGACAGCGTGGTGTCGGACCTGAGCCTGCACATGGTGCTGGAGGCCGGCGAGCACCGCGGCAGCTCGGTGACGGCGAAGGGCCG[C/T]
ATCGACATGGACGCCGGGGAGCGCGAGTCGGTGGTGATCGGCGGCACGGGGCGGTTTCGGCTCGCGCGCGGGTACATGGTCACCAAGAACTACGACTACA
TGTAGTCGTAGTTCTTGGTGACCATGTACCCGCGCGCGAGCCGAAACCGCCCCGTGCCGCCGATCACCACCGACTCGCGCTCCCCGGCGTCCATGTCGAT[G/A]
CGGCCCTTCGCCGTCACCGAGCTGCCGCGGTGCTCGCCGGCCTCCAGCACCATGTGCAGGCTCAGGTCCGACACCACGCTGTCGAAAAAAGATTTCGGCA
| 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 | 92.30% | 7.50% | 0.11% | 0.06% | NA |
| All Indica | 2759 | 91.30% | 8.60% | 0.11% | 0.00% | NA |
| All Japonica | 1512 | 92.70% | 6.90% | 0.13% | 0.20% | NA |
| Aus | 269 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica I | 595 | 98.70% | 0.80% | 0.50% | 0.00% | NA |
| Indica II | 465 | 97.00% | 3.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 84.90% | 15.10% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 89.70% | 10.30% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 99.00% | 0.50% | 0.26% | 0.26% | NA |
| Tropical Japonica | 504 | 82.50% | 17.30% | 0.00% | 0.20% | NA |
| Japonica Intermediate | 241 | 94.20% | 5.80% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 88.90% | 11.10% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1105974373 | C -> T | LOC_Os11g10840.1 | synonymous_variant ; p.Arg18Arg; LOW | synonymous_codon | Average:23.554; most accessible tissue: Callus, score: 34.526 | N | N | N | N |
| vg1105974373 | C -> DEL | LOC_Os11g10840.1 | N | frameshift_variant | Average:23.554; most accessible tissue: Callus, score: 34.526 | N | N | N | N |