| Variant ID: vg0139512590 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 39512590 |
| 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: 359. )
TGCGACGAGTCCTCCTCCTTCCAGCCTTGCCTCGGAGCTTCGATGGGTCAGGAATATTGAGTACTTCATCGTTAGTCTCTGTGAACTCCCCAGCTATGCC[G/A]
AACCCATAAATCTCGCCGCTCCATGTATGATATATTGCTTGCTTACTGAAGTACTGTGACACATATACTGCATCTGGTATGCCACACTCCGCTGCGGCAG
CTGCCGCAGCGGAGTGTGGCATACCAGATGCAGTATATGTGTCACAGTACTTCAGTAAGCAAGCAATATATCATACATGGAGCGGCGAGATTTATGGGTT[C/T]
GGCATAGCTGGGGAGTTCACAGAGACTAACGATGAAGTACTCAATATTCCTGACCCATCGAAGCTCCGAGGCAAGGCTGGAAGGAGGAGGACTCGTCGCA
| 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 | 10.00% | 0.10% | 13.27% | 76.66% | NA |
| All Indica | 2759 | 0.70% | 0.20% | 1.67% | 97.43% | NA |
| All Japonica | 1512 | 27.50% | 0.00% | 36.44% | 36.04% | NA |
| Aus | 269 | 2.20% | 0.00% | 0.00% | 97.77% | NA |
| Indica I | 595 | 1.20% | 0.00% | 1.34% | 97.48% | NA |
| Indica II | 465 | 0.20% | 0.00% | 0.86% | 98.92% | NA |
| Indica III | 913 | 0.90% | 0.00% | 0.55% | 98.58% | NA |
| Indica Intermediate | 786 | 0.50% | 0.60% | 3.69% | 95.17% | NA |
| Temperate Japonica | 767 | 36.50% | 0.00% | 46.41% | 17.08% | NA |
| Tropical Japonica | 504 | 21.20% | 0.00% | 27.38% | 51.39% | NA |
| Japonica Intermediate | 241 | 12.00% | 0.00% | 23.65% | 64.32% | NA |
| VI/Aromatic | 96 | 11.50% | 0.00% | 12.50% | 76.04% | NA |
| Intermediate | 90 | 20.00% | 0.00% | 20.00% | 60.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0139512590 | G -> A | LOC_Os01g67990.1 | synonymous_variant ; p.Phe768Phe; LOW | synonymous_codon | Average:10.696; most accessible tissue: Zhenshan97 root, score: 20.427 | N | N | N | N |
| vg0139512590 | G -> DEL | LOC_Os01g67990.1 | N | frameshift_variant | Average:10.696; most accessible tissue: Zhenshan97 root, score: 20.427 | N | N | N | N |