| Variant ID: vg1105160440 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 5160440 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.02, others allele: 0.00, population size: 59. )
CGGTCGTGTAGACTTGGAGAAACTCGGCGGGGTTGACGCTCCCGTCATATTTTTCGGCGATGGTGGGCCGGAACCTTGGGGGCCAACGGACGTTCCGAAG[G/A]
CTCGCCACAAAGGCTCTACAGCCGACACCACCAACCGGGGGCACGAAGGGCTGATCCCCGCGTCCGTGTTGATGTGACACTCCGGACGAGGAGGCGCCCT
AGGGCGCCTCCTCGTCCGGAGTGTCACATCAACACGGACGCGGGGATCAGCCCTTCGTGCCCCCGGTTGGTGGTGTCGGCTGTAGAGCCTTTGTGGCGAG[C/T]
CTTCGGAACGTCCGTTGGCCCCCAAGGTTCCGGCCCACCATCGCCGAAAAATATGACGGGAGCGTCAACCCCGCCGAGTTTCTCCAAGTCTACACGACCG
| 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 | 10.50% | 0.20% | 27.13% | 62.15% | NA |
| All Indica | 2759 | 1.00% | 0.40% | 27.18% | 71.48% | NA |
| All Japonica | 1512 | 29.80% | 0.00% | 27.71% | 42.46% | NA |
| Aus | 269 | 0.70% | 0.00% | 21.93% | 77.32% | NA |
| Indica I | 595 | 2.70% | 0.00% | 9.24% | 88.07% | NA |
| Indica II | 465 | 0.90% | 1.30% | 19.14% | 78.71% | NA |
| Indica III | 913 | 0.10% | 0.00% | 42.06% | 57.83% | NA |
| Indica Intermediate | 786 | 0.80% | 0.50% | 28.24% | 70.48% | NA |
| Temperate Japonica | 767 | 35.10% | 0.00% | 16.95% | 47.98% | NA |
| Tropical Japonica | 504 | 14.50% | 0.00% | 47.22% | 38.29% | NA |
| Japonica Intermediate | 241 | 45.20% | 0.00% | 21.16% | 33.61% | NA |
| VI/Aromatic | 96 | 5.20% | 0.00% | 32.29% | 62.50% | NA |
| Intermediate | 90 | 13.30% | 0.00% | 25.56% | 61.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1105160440 | G -> A | LOC_Os11g09660.1 | synonymous_variant ; p.Ser227Ser; LOW | synonymous_codon | Average:9.342; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |
| vg1105160440 | G -> DEL | LOC_Os11g09660.1 | N | frameshift_variant | Average:9.342; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |