| Variant ID: vg0142999150 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 42999150 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 101. )
CCACTCTTAGTCCGGCAAGGAGTCCCTCGTATTCTGCCATATTATTGGTCGCTCGAAAGTCGAGGCGGACCAAGTATCTGAGGACGTCTCCGCTCGGAGA[G/A]
GTCAACGTGACCCCCGCACCGGCGCCCTGAAGAGACAGGGAGCCGTCGAACTGCATCACCCAGTGGGCGGTGTGAGGCAGCTGCGAGGGGTCCGTGCTGG
CCAGCACGGACCCCTCGCAGCTGCCTCACACCGCCCACTGGGTGATGCAGTTCGACGGCTCCCTGTCTCTTCAGGGCGCCGGTGCGGGGGTCACGTTGAC[C/T]
TCTCCGAGCGGAGACGTCCTCAGATACTTGGTCCGCCTCGACTTTCGAGCGACCAATAATATGGCAGAATACGAGGGACTCCTTGCCGGACTAAGAGTGG
| 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 | 1.10% | 0.30% | 10.73% | 87.90% | NA |
| All Indica | 2759 | 1.30% | 0.20% | 8.77% | 89.67% | NA |
| All Japonica | 1512 | 0.70% | 0.00% | 8.86% | 90.41% | NA |
| Aus | 269 | 1.50% | 2.20% | 34.94% | 61.34% | NA |
| Indica I | 595 | 0.20% | 0.20% | 3.87% | 95.80% | NA |
| Indica II | 465 | 2.20% | 0.00% | 4.95% | 92.90% | NA |
| Indica III | 913 | 1.80% | 0.20% | 14.68% | 83.35% | NA |
| Indica Intermediate | 786 | 1.30% | 0.40% | 7.89% | 90.46% | NA |
| Temperate Japonica | 767 | 0.80% | 0.00% | 12.65% | 86.57% | NA |
| Tropical Japonica | 504 | 1.00% | 0.00% | 5.95% | 93.06% | NA |
| Japonica Intermediate | 241 | 0.00% | 0.00% | 2.90% | 97.10% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 21.88% | 78.12% | NA |
| Intermediate | 90 | 1.10% | 0.00% | 17.78% | 81.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0142999150 | G -> A | LOC_Os01g74230.1 | synonymous_variant ; p.Thr1284Thr; LOW | synonymous_codon | Average:6.478; most accessible tissue: Minghui63 root, score: 13.235 | N | N | N | N |
| vg0142999150 | G -> DEL | LOC_Os01g74230.1 | N | frameshift_variant | Average:6.478; most accessible tissue: Minghui63 root, score: 13.235 | N | N | N | N |