| Variant ID: vg0609017612 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 9017612 |
| 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: 122. )
CGGTAGTCGAGATGTCATGGCACAGGGCCGGTGTCCTGCTGCTAGGGGCTCAGTCCTGCCTGCCTGTCCCGGGGGTTCCGGCCGTAGGTGGGATTGGGTC[G/A]
GTACTCTTGTCTATGGCCAGGATGGGTTGGAAACTATGTCACGTCTTCCGTCTGTATACCGTGGTGGTATGTGGCACGTGGTTACACGTGAGGAAGATGT
ACATCTTCCTCACGTGTAACCACGTGCCACATACCACCACGGTATACAGACGGAAGACGTGACATAGTTTCCAACCCATCCTGGCCATAGACAAGAGTAC[C/T]
GACCCAATCCCACCTACGGCCGGAACCCCCGGGACAGGCAGGCAGGACTGAGCCCCTAGCAGCAGGACACCGGCCCTGTGCCATGACATCTCGACTACCG
| 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 | 32.40% | 0.40% | 16.42% | 50.80% | NA |
| All Indica | 2759 | 31.50% | 0.70% | 16.53% | 51.29% | NA |
| All Japonica | 1512 | 41.10% | 0.00% | 10.58% | 48.28% | NA |
| Aus | 269 | 1.50% | 0.00% | 37.55% | 60.97% | NA |
| Indica I | 595 | 21.80% | 0.20% | 18.82% | 59.16% | NA |
| Indica II | 465 | 40.90% | 0.90% | 24.95% | 33.33% | NA |
| Indica III | 913 | 31.30% | 0.50% | 8.87% | 59.26% | NA |
| Indica Intermediate | 786 | 33.60% | 1.00% | 18.70% | 46.69% | NA |
| Temperate Japonica | 767 | 73.00% | 0.00% | 1.83% | 25.16% | NA |
| Tropical Japonica | 504 | 5.40% | 0.00% | 20.24% | 74.40% | NA |
| Japonica Intermediate | 241 | 14.50% | 0.00% | 18.26% | 67.22% | NA |
| VI/Aromatic | 96 | 4.20% | 0.00% | 38.54% | 57.29% | NA |
| Intermediate | 90 | 34.40% | 0.00% | 24.44% | 41.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0609017612 | G -> A | LOC_Os06g15880.1 | synonymous_variant ; p.Ser30Ser; LOW | synonymous_codon | Average:23.747; most accessible tissue: Zhenshan97 flag leaf, score: 58.772 | N | N | N | N |
| vg0609017612 | G -> DEL | LOC_Os06g15880.1 | N | frameshift_variant | Average:23.747; most accessible tissue: Zhenshan97 flag leaf, score: 58.772 | N | N | N | N |