| Variant ID: vg0131446501 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 31446501 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TTCGGTGGGGCCGATCCTCTTCGCTAGGGGCCGCATCCCTGGGGCACTCTTCGTCCAAGCAGCCTCGCGGGGCGCACTTGTCTTCTGTGCTGATGACCTC[G/A]
GGGTCGGAGGATAACAGGGGCGGCCTTCCCACAGTGGCTTCGGGGCCGTCCTGGGGGTCGGGGGCTCCTGGCGTCGTCGGACAAGCGGGCAAAGGGCCAA
TTGGCCCTTTGCCCGCTTGTCCGACGACGCCAGGAGCCCCCGACCCCCAGGACGGCCCCGAAGCCACTGTGGGAAGGCCGCCCCTGTTATCCTCCGACCC[C/T]
GAGGTCATCAGCACAGAAGACAAGTGCGCCCCGCGAGGCTGCTTGGACGAAGAGTGCCCCAGGGATGCGGCCCCTAGCGAAGAGGATCGGCCCCACCGAA
| 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 | 10.10% | 0.10% | 18.54% | 71.27% | NA |
| All Indica | 2759 | 1.40% | 0.00% | 2.57% | 95.98% | NA |
| All Japonica | 1512 | 22.10% | 0.50% | 50.00% | 27.45% | NA |
| Aus | 269 | 0.70% | 0.00% | 0.00% | 99.26% | NA |
| Indica I | 595 | 2.70% | 0.00% | 1.01% | 96.30% | NA |
| Indica II | 465 | 0.40% | 0.00% | 0.22% | 99.35% | NA |
| Indica III | 913 | 0.00% | 0.00% | 4.60% | 95.40% | NA |
| Indica Intermediate | 786 | 2.80% | 0.00% | 2.80% | 94.40% | NA |
| Temperate Japonica | 767 | 30.40% | 0.00% | 40.81% | 28.81% | NA |
| Tropical Japonica | 504 | 12.70% | 1.40% | 73.41% | 12.50% | NA |
| Japonica Intermediate | 241 | 15.40% | 0.00% | 30.29% | 54.36% | NA |
| VI/Aromatic | 96 | 82.30% | 0.00% | 12.50% | 5.21% | NA |
| Intermediate | 90 | 22.20% | 0.00% | 41.11% | 36.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0131446501 | G -> A | LOC_Os01g54660.1 | synonymous_variant ; p.Pro1278Pro; LOW | synonymous_codon | Average:10.984; most accessible tissue: Zhenshan97 flag leaf, score: 24.112 | N | N | N | N |
| vg0131446501 | G -> DEL | LOC_Os01g54660.1 | N | frameshift_variant | Average:10.984; most accessible tissue: Zhenshan97 flag leaf, score: 24.112 | N | N | N | N |