| Variant ID: vg0904848027 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 4848027 |
| 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: 281. )
CTCTACCTCCATTAGCTAAAAGATGCTCTGTCAACTGTTGTGCACCTCGGGAGGAATTTCTTCTCTGACATTTTGTCATTCCTGGTGGAGGCCATTCTGT[G/A]
CTGGTAATGATCATCTTACGGACTTCATCTTCGGTTCGCATTGGTGCTTTTCTTTTCTGCTGAGGACAGTTCCTTGCATAGTGCCCTTGCTCATCACACA
TGTGTGATGAGCAAGGGCACTATGCAAGGAACTGTCCTCAGCAGAAAAGAAAAGCACCAATGCGAACCGAAGATGAAGTCCGTAAGATGATCATTACCAG[C/T]
ACAGAATGGCCTCCACCAGGAATGACAAAATGTCAGAGAAGAAATTCCTCCCGAGGTGCACAACAGTTGACAGAGCATCTTTTAGCTAATGGAGGTAGAG
| 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 | 16.90% | 0.40% | 3.09% | 79.62% | NA |
| All Indica | 2759 | 4.60% | 0.00% | 1.85% | 93.55% | NA |
| All Japonica | 1512 | 34.00% | 1.30% | 5.16% | 59.59% | NA |
| Aus | 269 | 21.20% | 0.00% | 2.23% | 76.58% | NA |
| Indica I | 595 | 5.50% | 0.00% | 1.18% | 93.28% | NA |
| Indica II | 465 | 6.20% | 0.00% | 0.43% | 93.33% | NA |
| Indica III | 913 | 1.80% | 0.00% | 1.97% | 96.28% | NA |
| Indica Intermediate | 786 | 6.10% | 0.10% | 3.05% | 90.71% | NA |
| Temperate Japonica | 767 | 39.50% | 2.20% | 2.74% | 55.54% | NA |
| Tropical Japonica | 504 | 25.00% | 0.00% | 4.56% | 70.44% | NA |
| Japonica Intermediate | 241 | 35.30% | 0.80% | 14.11% | 49.79% | NA |
| VI/Aromatic | 96 | 78.10% | 0.00% | 8.33% | 13.54% | NA |
| Intermediate | 90 | 27.80% | 0.00% | 3.33% | 68.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0904848027 | G -> DEL | LOC_Os09g09070.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0904848027 | G -> A | LOC_Os09g09070.1 | synonymous_variant ; p.Ser137Ser; LOW | synonymous_codon | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |