| Variant ID: vg0903742152 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 3742152 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.73, G: 0.27, others allele: 0.00, population size: 222. )
GAGGTTGATGGGCCTTCTTGATGATGCATTTTGAGGAGTACGGTCCAGGTCTCGACTAGGGTGGGGACCGTGGGCGTCCTCGGCAACTTCGTTCTCCGTT[A/G]
CTCTGTCATCGGTATGTTGTCGGGGATCTCGAGCAGGACCTTGCGGGGTTGGTTCGGCTGCGGTCAAGAAAGCAGAGTTGAGGTTGGCTATTGTCGACTA
TAGTCGACAATAGCCAACCTCAACTCTGCTTTCTTGACCGCAGCCGAACCAACCCCGCAAGGTCCTGCTCGAGATCCCCGACAACATACCGATGACAGAG[T/C]
AACGGAGAACGAAGTTGCCGAGGACGCCCACGGTCCCCACCCTAGTCGAGACCTGGACCGTACTCCTCAAAATGCATCATCAAGAAGGCCCATCAACCTC
| 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 | 62.90% | 37.10% | 0.02% | 0.02% | NA |
| All Indica | 2759 | 95.80% | 4.10% | 0.00% | 0.04% | NA |
| All Japonica | 1512 | 0.90% | 99.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 99.30% | 0.70% | 0.00% | 0.00% | NA |
| Indica I | 595 | 94.50% | 5.40% | 0.00% | 0.17% | NA |
| Indica II | 465 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
| Indica III | 913 | 97.40% | 2.60% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 93.30% | 6.70% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 0.70% | 99.30% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 1.00% | 99.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 1.20% | 98.80% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 6.20% | 93.80% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 46.70% | 52.20% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0903742152 | A -> G | LOC_Os09g07470.1 | stop_lost&splice_region_variant ; p.Ter129Glnext*?; HIGH | stop_lost | Average:73.803; most accessible tissue: Zhenshan97 young leaf, score: 88.995 | N | N | N | N |
| vg0903742152 | A -> DEL | LOC_Os09g07470.1 | N | frameshift_variant | Average:73.803; most accessible tissue: Zhenshan97 young leaf, score: 88.995 | N | N | N | N |