| Variant ID: vg0904847977 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 4847977 |
| 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: 291. )
CTCATCTTCATCATCTGAGGAGACTTGATCTGAATCTTCACTACCAGACACTCTACCTCCATTAGCTAAAAGATGCTCTGTCAACTGTTGTGCACCTCGG[G/A]
AGGAATTTCTTCTCTGACATTTTGTCATTCCTGGTGGAGGCCATTCTGTGCTGGTAATGATCATCTTACGGACTTCATCTTCGGTTCGCATTGGTGCTTT
AAAGCACCAATGCGAACCGAAGATGAAGTCCGTAAGATGATCATTACCAGCACAGAATGGCCTCCACCAGGAATGACAAAATGTCAGAGAAGAAATTCCT[C/T]
CCGAGGTGCACAACAGTTGACAGAGCATCTTTTAGCTAATGGAGGTAGAGTGTCTGGTAGTGAAGATTCAGATCAAGTCTCCTCAGATGATGAAGATGAG
| 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 | 17.20% | 0.60% | 3.07% | 79.20% | NA |
| All Indica | 2759 | 4.80% | 0.00% | 1.96% | 93.22% | NA |
| All Japonica | 1512 | 34.10% | 1.70% | 5.49% | 58.73% | NA |
| Aus | 269 | 21.60% | 0.00% | 1.12% | 77.32% | NA |
| Indica I | 595 | 5.20% | 0.00% | 0.84% | 93.95% | NA |
| Indica II | 465 | 6.20% | 0.00% | 0.43% | 93.33% | NA |
| Indica III | 913 | 1.90% | 0.00% | 2.30% | 95.84% | NA |
| Indica Intermediate | 786 | 7.00% | 0.10% | 3.31% | 89.57% | NA |
| Temperate Japonica | 767 | 39.10% | 3.00% | 2.74% | 55.15% | NA |
| Tropical Japonica | 504 | 24.80% | 0.00% | 6.15% | 69.05% | NA |
| Japonica Intermediate | 241 | 37.30% | 1.20% | 12.86% | 48.55% | NA |
| VI/Aromatic | 96 | 83.30% | 0.00% | 3.12% | 13.54% | NA |
| Intermediate | 90 | 28.90% | 0.00% | 2.22% | 68.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0904847977 | G -> DEL | LOC_Os09g09070.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0904847977 | G -> A | LOC_Os09g09070.1 | missense_variant ; p.Ser154Phe; MODERATE | nonsynonymous_codon ; S154F | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | unknown | unknown | TOLERATED | 1.00 |