| Variant ID: vg0904848031 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 4848031 |
| 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: 286. )
ACCTCCATTAGCTAAAAGATGCTCTGTCAACTGTTGTGCACCTCGGGAGGAATTTCTTCTCTGACATTTTGTCATTCCTGGTGGAGGCCATTCTGTGCTG[G/A]
TAATGATCATCTTACGGACTTCATCTTCGGTTCGCATTGGTGCTTTTCTTTTCTGCTGAGGACAGTTCCTTGCATAGTGCCCTTGCTCATCACACATAAA
TTTATGTGTGATGAGCAAGGGCACTATGCAAGGAACTGTCCTCAGCAGAAAAGAAAAGCACCAATGCGAACCGAAGATGAAGTCCGTAAGATGATCATTA[C/T]
CAGCACAGAATGGCCTCCACCAGGAATGACAAAATGTCAGAGAAGAAATTCCTCCCGAGGTGCACAACAGTTGACAGAGCATCTTTTAGCTAATGGAGGT
| 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 | 14.30% | 0.60% | 2.73% | 82.42% | NA |
| All Indica | 2759 | 3.20% | 0.10% | 0.51% | 96.19% | NA |
| All Japonica | 1512 | 33.00% | 0.10% | 5.62% | 61.31% | NA |
| Aus | 269 | 14.50% | 1.10% | 1.86% | 82.53% | NA |
| Indica I | 595 | 6.20% | 0.00% | 0.50% | 93.28% | NA |
| Indica II | 465 | 4.10% | 0.00% | 0.43% | 95.48% | NA |
| Indica III | 913 | 0.50% | 0.10% | 0.11% | 99.23% | NA |
| Indica Intermediate | 786 | 3.60% | 0.10% | 1.02% | 95.29% | NA |
| Temperate Japonica | 767 | 42.60% | 0.00% | 1.69% | 55.67% | NA |
| Tropical Japonica | 504 | 20.40% | 0.00% | 4.96% | 74.60% | NA |
| Japonica Intermediate | 241 | 28.60% | 0.40% | 19.50% | 51.45% | NA |
| VI/Aromatic | 96 | 30.20% | 20.80% | 21.88% | 27.08% | NA |
| Intermediate | 90 | 20.00% | 2.20% | 4.44% | 73.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0904848031 | G -> DEL | LOC_Os09g09070.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0904848031 | G -> A | LOC_Os09g09070.1 | missense_variant ; p.Thr136Ile; MODERATE | nonsynonymous_codon ; T136I | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | unknown | unknown | DELETERIOUS | 0.00 |