| Variant ID: vg0826581373 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 26581373 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GATGCACTGAGGCCGGATAAATTCACCGGTGTGCATTTTAAGAGATGGCAGATCAGGGTCACTCTGTGGCTGACAGCTATGAAATGCTTCTGGGTGAGTA[C/T]
TGGCAAACCTGAAGGAGTTCTTACTGCTGAACAACAGAAGCAATTCGAGGAAGCTACTACTCTCTTTGTGGGATGCATTCTTAGCGTTCTTGGCGATTGT
ACAATCGCCAAGAACGCTAAGAATGCATCCCACAAAGAGAGTAGTAGCTTCCTCGAATTGCTTCTGTTGTTCAGCAGTAAGAACTCCTTCAGGTTTGCCA[G/A]
TACTCACCCAGAAGCATTTCATAGCTGTCAGCCACAGAGTGACCCTGATCTGCCATCTCTTAAAATGCACACCGGTGAATTTATCCGGCCTCAGTGCATC
| 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 | 31.00% | 0.30% | 8.36% | 60.33% | NA |
| All Indica | 2759 | 3.00% | 0.00% | 13.48% | 83.47% | NA |
| All Japonica | 1512 | 81.30% | 0.60% | 1.06% | 17.06% | NA |
| Aus | 269 | 8.60% | 0.00% | 0.37% | 91.08% | NA |
| Indica I | 595 | 2.00% | 0.00% | 8.91% | 89.08% | NA |
| Indica II | 465 | 2.80% | 0.20% | 6.45% | 90.54% | NA |
| Indica III | 913 | 3.70% | 0.00% | 21.14% | 75.14% | NA |
| Indica Intermediate | 786 | 3.10% | 0.00% | 12.21% | 84.73% | NA |
| Temperate Japonica | 767 | 94.70% | 0.00% | 0.26% | 5.08% | NA |
| Tropical Japonica | 504 | 70.20% | 1.80% | 1.59% | 26.39% | NA |
| Japonica Intermediate | 241 | 61.80% | 0.00% | 2.49% | 35.68% | NA |
| VI/Aromatic | 96 | 93.80% | 0.00% | 0.00% | 6.25% | NA |
| Intermediate | 90 | 43.30% | 6.70% | 6.67% | 43.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0826581373 | C -> T | LOC_Os08g42090.1 | missense_variant ; p.Thr39Ile; MODERATE | nonsynonymous_codon ; T39I | Average:6.326; most accessible tissue: Zhenshan97 flower, score: 11.396 | unknown | unknown | DELETERIOUS | 0.02 |
| vg0826581373 | C -> DEL | LOC_Os08g42090.1 | N | frameshift_variant | Average:6.326; most accessible tissue: Zhenshan97 flower, score: 11.396 | N | N | N | N |