| Variant ID: vg1117778415 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 17778415 |
| 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: 390. )
CTAACAGATGCAGTGGAAGCCTCCTCTCAGGGCACGTTCCGACCAGACAGAGATAGGGACGAGCTGACACTCGCCCTGCAGACTCCAGAGCATCCAGGAC[G/A]
AACACGAGGGAAAGGGGTGATTCCTTGGAAGATTGGTTTCAAGGAGGACATCCACACGTACAGGAGTCGGATGAGGAGCAAGAGAGATACCGAGGCGAAG
CTTCGCCTCGGTATCTCTCTTGCTCCTCATCCGACTCCTGTACGTGTGGATGTCCTCCTTGAAACCAATCTTCCAAGGAATCACCCCTTTCCCTCGTGTT[C/T]
GTCCTGGATGCTCTGGAGTCTGCAGGGCGAGTGTCAGCTCGTCCCTATCTCTGTCTGGTCGGAACGTGCCCTGAGAGGAGGCTTCCACTGCATCTGTTAG
| 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 | 12.30% | 0.40% | 12.25% | 74.99% | NA |
| All Indica | 2759 | 7.80% | 0.80% | 4.71% | 86.73% | NA |
| All Japonica | 1512 | 21.60% | 0.00% | 24.74% | 53.70% | NA |
| Aus | 269 | 4.80% | 0.00% | 13.01% | 82.16% | NA |
| Indica I | 595 | 3.50% | 1.00% | 3.70% | 91.76% | NA |
| Indica II | 465 | 18.90% | 0.00% | 3.44% | 77.63% | NA |
| Indica III | 913 | 6.80% | 1.10% | 6.24% | 85.87% | NA |
| Indica Intermediate | 786 | 5.60% | 0.60% | 4.45% | 89.31% | NA |
| Temperate Japonica | 767 | 18.40% | 0.00% | 30.90% | 50.72% | NA |
| Tropical Japonica | 504 | 16.10% | 0.00% | 11.31% | 72.62% | NA |
| Japonica Intermediate | 241 | 43.20% | 0.00% | 33.20% | 23.65% | NA |
| VI/Aromatic | 96 | 14.60% | 0.00% | 30.21% | 55.21% | NA |
| Intermediate | 90 | 15.60% | 0.00% | 12.22% | 72.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1117778415 | G -> A | LOC_Os11g30552.1 | missense_variant ; p.Arg456Gln; MODERATE | nonsynonymous_codon ; R456Q | Average:8.249; most accessible tissue: Zhenshan97 panicle, score: 16.188 | unknown | unknown | DELETERIOUS | 0.04 |
| vg1117778415 | G -> DEL | LOC_Os11g30552.1 | N | frameshift_variant | Average:8.249; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |