| Variant ID: vg0131448228 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 31448228 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GCTGCTCCAGACAAGCGAGCGCGACTTTGAGGTCGCCATGGACAGAGATGGGGCCACCGGGGCCCGACATCTTCATCTGTAGGTAGGCGTAGTGGACCGC[C/T]
GCCATGAACTTCACCAACGCGGGCCTCCCCAGGACCGCGTTGTAGGGCAGACTGAGGTCCGCCACATCGAAGTTCACCCGCTCCGTGCGGAAGTTGGCGG
CCGCCAACTTCCGCACGGAGCGGGTGAACTTCGATGTGGCGGACCTCAGTCTGCCCTACAACGCGGTCCTGGGGAGGCCCGCGTTGGTGAAGTTCATGGC[G/A]
GCGGTCCACTACGCCTACCTACAGATGAAGATGTCGGGCCCCGGTGGCCCCATCTCTGTCCATGGCGACCTCAAAGTCGCGCTCGCTTGTCTGGAGCAGC
| 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 | 53.40% | 1.40% | 7.64% | 37.58% | NA |
| All Indica | 2759 | 36.70% | 2.40% | 12.54% | 48.31% | NA |
| All Japonica | 1512 | 84.60% | 0.00% | 0.53% | 14.88% | NA |
| Aus | 269 | 25.70% | 0.00% | 1.12% | 73.23% | NA |
| Indica I | 595 | 27.70% | 1.50% | 8.40% | 62.35% | NA |
| Indica II | 465 | 22.20% | 2.40% | 11.61% | 63.87% | NA |
| Indica III | 913 | 50.50% | 3.90% | 14.90% | 30.67% | NA |
| Indica Intermediate | 786 | 36.10% | 1.40% | 13.49% | 48.98% | NA |
| Temperate Japonica | 767 | 87.90% | 0.00% | 0.13% | 11.99% | NA |
| Tropical Japonica | 504 | 91.30% | 0.00% | 0.40% | 8.33% | NA |
| Japonica Intermediate | 241 | 60.20% | 0.00% | 2.07% | 37.76% | NA |
| VI/Aromatic | 96 | 97.90% | 0.00% | 0.00% | 2.08% | NA |
| Intermediate | 90 | 74.40% | 0.00% | 4.44% | 21.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0131448228 | C -> T | LOC_Os01g54660.1 | synonymous_variant ; p.Ala715Ala; LOW | synonymous_codon | Average:38.542; most accessible tissue: Zhenshan97 panicle, score: 71.253 | N | N | N | N |
| vg0131448228 | C -> DEL | LOC_Os01g54660.1 | N | frameshift_variant | Average:38.542; most accessible tissue: Zhenshan97 panicle, score: 71.253 | N | N | N | N |