| Variant ID: vg0609242047 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 9242047 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 113. )
AGGCGTAGTGGACCGCCGCCATGAACTTCACCAACGCGGGTCTCCCCAGGACCGCGTTGTAGGGCAGACTGAGGTCCGCCACATCGAAGCTCACCCGCTC[C/A]
GTGCGGAAGTTGGCGGGTCCACCGAAGGTGACCGGTAGGTCAATGTGACCTAATGGCCACGTGTGCCCCGGCGTCACACCGATGATCGGTTGAGACGGCT
AGCCGTCTCAACCGATCATCGGTGTGACGCCGGGGCACACGTGGCCATTAGGTCACATTGACCTACCGGTCACCTTCGGTGGACCCGCCAACTTCCGCAC[G/T]
GAGCGGGTGAGCTTCGATGTGGCGGACCTCAGTCTGCCCTACAACGCGGTCCTGGGGAGACCCGCGTTGGTGAAGTTCATGGCGGCGGTCCACTACGCCT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 12.40% | 0.40% | 3.34% | 83.86% | NA |
| All Indica | 2759 | 1.10% | 0.70% | 1.12% | 97.10% | NA |
| All Japonica | 1512 | 36.10% | 0.00% | 0.26% | 63.62% | NA |
| Aus | 269 | 0.00% | 0.00% | 42.75% | 57.25% | NA |
| Indica I | 595 | 1.30% | 0.00% | 0.50% | 98.15% | NA |
| Indica II | 465 | 1.10% | 0.40% | 0.86% | 97.63% | NA |
| Indica III | 913 | 0.20% | 0.90% | 1.10% | 97.81% | NA |
| Indica Intermediate | 786 | 2.00% | 1.00% | 1.78% | 95.17% | NA |
| Temperate Japonica | 767 | 67.40% | 0.00% | 0.39% | 32.20% | NA |
| Tropical Japonica | 504 | 1.80% | 0.00% | 0.00% | 98.21% | NA |
| Japonica Intermediate | 241 | 8.30% | 0.00% | 0.41% | 91.29% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 6.25% | 93.75% | NA |
| Intermediate | 90 | 11.10% | 0.00% | 2.22% | 86.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0609242047 | C -> A | LOC_Os06g16230.1 | synonymous_variant ; p.Thr688Thr; LOW | synonymous_codon | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0609242047 | C -> DEL | LOC_Os06g16230.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |