| Variant ID: vg0128509357 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 28509357 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TATGTCCTGGGACTGGTACTGAGATCACGGTTTCGTAGGAAGCGGTTCGCGCCGTTTTTCCCACGACACGCTCCTGTCAGGTGCCGTTGTACGGCGGTGC[C/T]
AGATTGGGGTGTGACATATATGAACGATGGGAGGCGCGTGATGGTGGCGGTGTCTAGGCCGAACCTGGGCAGCGTCGGCTGCTGCTGCTCCTGCTCCATG
CATGGAGCAGGAGCAGCAGCAGCCGACGCTGCCCAGGTTCGGCCTAGACACCGCCACCATCACGCGCCTCCCATCGTTCATATATGTCACACCCCAATCT[G/A]
GCACCGCCGTACAACGGCACCTGACAGGAGCGTGTCGTGGGAAAAACGGCGCGAACCGCTTCCTACGAAACCGTGATCTCAGTACCAGTCCCAGGACATA
| 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 | 30.60% | 0.10% | 15.47% | 53.77% | NA |
| All Indica | 2759 | 8.50% | 0.10% | 16.67% | 74.74% | NA |
| All Japonica | 1512 | 75.70% | 0.10% | 7.34% | 16.93% | NA |
| Aus | 269 | 7.80% | 0.70% | 50.19% | 41.26% | NA |
| Indica I | 595 | 11.60% | 0.00% | 4.87% | 83.53% | NA |
| Indica II | 465 | 6.00% | 0.00% | 7.31% | 86.67% | NA |
| Indica III | 913 | 8.40% | 0.00% | 31.43% | 60.13% | NA |
| Indica Intermediate | 786 | 7.80% | 0.30% | 13.99% | 77.99% | NA |
| Temperate Japonica | 767 | 99.30% | 0.00% | 0.13% | 0.52% | NA |
| Tropical Japonica | 504 | 33.50% | 0.20% | 20.44% | 45.83% | NA |
| Japonica Intermediate | 241 | 88.40% | 0.00% | 2.90% | 8.71% | NA |
| VI/Aromatic | 96 | 14.60% | 0.00% | 10.42% | 75.00% | NA |
| Intermediate | 90 | 36.70% | 2.20% | 16.67% | 44.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0128509357 | C -> T | LOC_Os01g49570.1 | missense_variant ; p.Gly73Ser; MODERATE | nonsynonymous_codon ; G73S | Average:21.886; most accessible tissue: Zhenshan97 panicle, score: 39.652 | unknown | unknown | TOLERATED | 0.10 |
| vg0128509357 | C -> DEL | LOC_Os01g49570.1 | N | frameshift_variant | Average:21.886; most accessible tissue: Zhenshan97 panicle, score: 39.652 | N | N | N | N |