| Variant ID: vg0903742156 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 3742156 |
| Reference Allele: T | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.93, T: 0.07, others allele: 0.00, population size: 245. )
TTGATGGGCCTTCTTGATGATGCATTTTGAGGAGTACGGTCCAGGTCTCGACTAGGGTGGGGACCGTGGGCGTCCTCGGCAACTTCGTTCTCCGTTACTC[T/G]
GTCATCGGTATGTTGTCGGGGATCTCGAGCAGGACCTTGCGGGGTTGGTTCGGCTGCGGTCAAGAAAGCAGAGTTGAGGTTGGCTATTGTCGACTATATA
TATATAGTCGACAATAGCCAACCTCAACTCTGCTTTCTTGACCGCAGCCGAACCAACCCCGCAAGGTCCTGCTCGAGATCCCCGACAACATACCGATGAC[A/C]
GAGTAACGGAGAACGAAGTTGCCGAGGACGCCCACGGTCCCCACCCTAGTCGAGACCTGGACCGTACTCCTCAAAATGCATCATCAAGAAGGCCCATCAA
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 65.00% | 35.00% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 97.40% | 2.60% | 0.00% | 0.00% | 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 | 95.10% | 4.90% | 0.00% | 0.00% | NA |
| Indica II | 465 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 96.40% | 3.60% | 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 | 1.70% | 98.30% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 56.20% | 43.80% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 53.30% | 46.70% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0903742156 | T -> G | LOC_Os09g07470.1 | synonymous_variant ; p.Thr127Thr; LOW | synonymous_codon | Average:73.764; most accessible tissue: Zhenshan97 young leaf, score: 88.995 | N | N | N | N |