| Variant ID: vg0609017552 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 9017552 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 272. )
ATGAAGTCGGGGGTCGATGGACATTCTCCAGGGCAAATGAAGGCTACACGGGCTGCGGTTCGGTAGTCGAGATGTCATGGCACAGGGCCGGTGTCCTGCT[G/A]
CTAGGGGCTCAGTCCTGCCTGCCTGTCCCGGGGGTTCCGGCCGTAGGTGGGATTGGGTCGGTACTCTTGTCTATGGCCAGGATGGGTTGGAAACTATGTC
GACATAGTTTCCAACCCATCCTGGCCATAGACAAGAGTACCGACCCAATCCCACCTACGGCCGGAACCCCCGGGACAGGCAGGCAGGACTGAGCCCCTAG[C/T]
AGCAGGACACCGGCCCTGTGCCATGACATCTCGACTACCGAACCGCAGCCCGTGTAGCCTTCATTTGCCCTGGAGAATGTCCATCGACCCCCGACTTCAT
| 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 | 52.10% | 0.10% | 14.92% | 32.88% | NA |
| All Indica | 2759 | 60.00% | 0.20% | 10.37% | 29.39% | NA |
| All Japonica | 1512 | 42.20% | 0.00% | 14.48% | 43.32% | NA |
| Aus | 269 | 40.90% | 0.00% | 52.04% | 7.06% | NA |
| Indica I | 595 | 57.10% | 0.20% | 3.70% | 38.99% | NA |
| Indica II | 465 | 79.10% | 0.40% | 7.96% | 12.47% | NA |
| Indica III | 913 | 46.00% | 0.20% | 16.10% | 37.68% | NA |
| Indica Intermediate | 786 | 67.20% | 0.10% | 10.18% | 22.52% | NA |
| Temperate Japonica | 767 | 73.50% | 0.00% | 3.00% | 23.47% | NA |
| Tropical Japonica | 504 | 8.50% | 0.00% | 26.98% | 64.48% | NA |
| Japonica Intermediate | 241 | 12.90% | 0.00% | 24.90% | 62.24% | NA |
| VI/Aromatic | 96 | 9.40% | 0.00% | 44.79% | 45.83% | NA |
| Intermediate | 90 | 53.30% | 0.00% | 18.89% | 27.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0609017552 | G -> A | LOC_Os06g15880.1 | synonymous_variant ; p.Leu10Leu; LOW | synonymous_codon | Average:19.447; most accessible tissue: Zhenshan97 flower, score: 52.192 | N | N | N | N |
| vg0609017552 | G -> DEL | LOC_Os06g15880.1 | N | frameshift_variant | Average:19.447; most accessible tissue: Zhenshan97 flower, score: 52.192 | N | N | N | N |