| Variant ID: vg1126361847 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 26361847 |
| 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: 78. )
GCCAACTTGGTCATGACGGCACAGCAACGCCTGGGTGCTGGCGGACGGTCCGCCACCACCAAGACCTCCGGCGCCGCCACTACCGGTTCCGCGTCGTCAA[G/A]
ACGGAGGGCGCGGCGAGCGGCGGCTGCTGCACGCCATTCGGCTACCACTCCCTCGTCGGCGCCTCCGACTCGGGAGGATCAGCATGAAGAGCCGGATGCC
GGCATCCGGCTCTTCATGCTGATCCTCCCGAGTCGGAGGCGCCGACGAGGGAGTGGTAGCCGAATGGCGTGCAGCAGCCGCCGCTCGCCGCGCCCTCCGT[C/T]
TTGACGACGCGGAACCGGTAGTGGCGGCGCCGGAGGTCTTGGTGGTGGCGGACCGTCCGCCAGCACCCAGGCGTTGCTGTGCCGTCATGACCAAGTTGGC
| 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 | 30.80% | 0.30% | 15.26% | 53.64% | NA |
| All Indica | 2759 | 11.90% | 0.20% | 15.66% | 72.27% | NA |
| All Japonica | 1512 | 63.80% | 0.50% | 11.97% | 23.74% | NA |
| Aus | 269 | 30.50% | 0.00% | 33.46% | 36.06% | NA |
| Indica I | 595 | 6.60% | 0.00% | 8.24% | 85.21% | NA |
| Indica II | 465 | 8.00% | 0.00% | 12.26% | 79.78% | NA |
| Indica III | 913 | 14.60% | 0.40% | 19.82% | 65.17% | NA |
| Indica Intermediate | 786 | 15.10% | 0.10% | 18.45% | 66.28% | NA |
| Temperate Japonica | 767 | 52.00% | 0.10% | 9.78% | 38.07% | NA |
| Tropical Japonica | 504 | 82.50% | 0.40% | 10.32% | 6.75% | NA |
| Japonica Intermediate | 241 | 61.80% | 2.10% | 22.41% | 13.69% | NA |
| VI/Aromatic | 96 | 45.80% | 0.00% | 9.38% | 44.79% | NA |
| Intermediate | 90 | 43.30% | 0.00% | 10.00% | 46.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1126361847 | G -> A | LOC_Os11g43670.1 | missense_variant ; p.Arg143Lys; MODERATE | nonsynonymous_codon ; R143K | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | unknown | unknown | DELETERIOUS | 0.00 |
| vg1126361847 | G -> DEL | LOC_Os11g43670.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |