| Variant ID: vg0128724425 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 28724425 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GCGTGCTAACTCCAGGAGTTAGCACACCGGCTCCGGCTAGGGACGAGTGCCTGGAGGCTCTCATCATTCCGACGGGACGGGGCGAGGCGTGTGACAGGCC[G/A]
CCTGCTGCCACCTAACCCGCGATCCGACCGATCTGTGACTGGTCACATACTGCGACCGGTCACGGACCGGATAAGCGAGCGCGCTGCGCTGTATTAAATG
CATTTAATACAGCGCAGCGCGCTCGCTTATCCGGTCCGTGACCGGTCGCAGTATGTGACCAGTCACAGATCGGTCGGATCGCGGGTTAGGTGGCAGCAGG[C/T]
GGCCTGTCACACGCCTCGCCCCGTCCCGTCGGAATGATGAGAGCCTCCAGGCACTCGTCCCTAGCCGGAGCCGGTGTGCTAACTCCTGGAGTTAGCACGC
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 27.30% | 2.60% | 11.45% | 58.65% | NA |
| All Indica | 2759 | 2.40% | 0.00% | 14.17% | 83.47% | NA |
| All Japonica | 1512 | 76.40% | 7.80% | 1.98% | 13.82% | NA |
| Aus | 269 | 6.30% | 0.00% | 42.38% | 51.30% | NA |
| Indica I | 595 | 0.80% | 0.00% | 2.86% | 96.30% | NA |
| Indica II | 465 | 3.40% | 0.00% | 12.69% | 83.87% | NA |
| Indica III | 913 | 1.50% | 0.00% | 21.58% | 76.89% | NA |
| Indica Intermediate | 786 | 3.80% | 0.00% | 15.01% | 81.17% | NA |
| Temperate Japonica | 767 | 97.80% | 0.00% | 1.56% | 0.65% | NA |
| Tropical Japonica | 504 | 36.90% | 23.00% | 2.58% | 37.50% | NA |
| Japonica Intermediate | 241 | 90.90% | 0.80% | 2.07% | 6.22% | NA |
| VI/Aromatic | 96 | 14.60% | 2.10% | 4.17% | 79.17% | NA |
| Intermediate | 90 | 43.30% | 3.30% | 2.22% | 51.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0128724425 | G -> A | LOC_Os01g49990.1 | synonymous_variant ; p.Pro106Pro; LOW | synonymous_codon | Average:17.918; most accessible tissue: Minghui63 panicle, score: 25.313 | N | N | N | N |
| vg0128724425 | G -> DEL | LOC_Os01g49990.1 | N | frameshift_variant | Average:17.918; most accessible tissue: Minghui63 panicle, score: 25.313 | N | N | N | N |