| Variant ID: vg0128509318 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 28509318 |
| Reference Allele: C | Alternative Allele: G,T |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
ATTGCAATTATTCATATTTGTCACCGTGGGTACCAGCGCTATGTCCTGGGACTGGTACTGAGATCACGGTTTCGTAGGAAGCGGTTCGCGCCGTTTTTCC[C/G,T]
ACGACACGCTCCTGTCAGGTGCCGTTGTACGGCGGTGCCAGATTGGGGTGTGACATATATGAACGATGGGAGGCGCGTGATGGTGGCGGTGTCTAGGCCG
CGGCCTAGACACCGCCACCATCACGCGCCTCCCATCGTTCATATATGTCACACCCCAATCTGGCACCGCCGTACAACGGCACCTGACAGGAGCGTGTCGT[G/C,A]
GGAAAAACGGCGCGAACCGCTTCCTACGAAACCGTGATCTCAGTACCAGTCCCAGGACATAGCGCTGGTACCCACGGTGACAAATATGAATAATTGCAAT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 27.20% | 1.10% | 10.83% | 60.73% | T: 0.06% |
| All Indica | 2759 | 4.30% | 0.00% | 11.60% | 83.98% | T: 0.07% |
| All Japonica | 1512 | 73.00% | 3.40% | 2.58% | 21.03% | NA |
| Aus | 269 | 5.60% | 0.00% | 50.56% | 43.49% | T: 0.37% |
| Indica I | 595 | 4.40% | 0.00% | 1.51% | 93.95% | T: 0.17% |
| Indica II | 465 | 2.80% | 0.00% | 4.30% | 92.90% | NA |
| Indica III | 913 | 6.00% | 0.00% | 25.63% | 68.35% | NA |
| Indica Intermediate | 786 | 3.20% | 0.10% | 7.25% | 89.31% | T: 0.13% |
| Temperate Japonica | 767 | 92.70% | 6.60% | 0.00% | 0.65% | NA |
| Tropical Japonica | 504 | 35.70% | 0.00% | 6.94% | 57.34% | NA |
| Japonica Intermediate | 241 | 88.40% | 0.00% | 1.66% | 9.96% | NA |
| VI/Aromatic | 96 | 17.70% | 0.00% | 7.29% | 75.00% | NA |
| Intermediate | 90 | 35.60% | 2.20% | 11.11% | 51.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0128509318 | C -> G | LOC_Os01g49570.1 | missense_variant ; p.Gly86Arg; MODERATE | nonsynonymous_codon ; G86R | Average:20.672; most accessible tissue: Zhenshan97 panicle, score: 28.447 | unknown | unknown | TOLERATED | 1.00 |
| vg0128509318 | C -> T | LOC_Os01g49570.1 | missense_variant ; p.Gly86Arg; MODERATE | nonsynonymous_codon ; G86R | Average:20.672; most accessible tissue: Zhenshan97 panicle, score: 28.447 | unknown | unknown | TOLERATED | 1.00 |
| vg0128509318 | C -> DEL | LOC_Os01g49570.1 | N | frameshift_variant | Average:20.672; most accessible tissue: Zhenshan97 panicle, score: 28.447 | N | N | N | N |