| Variant ID: vg1105183588 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 5183588 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 259. )
GATACCTTGCTTCAAAATAAGTGTGTTGATTTACCTCCAATCCCACGTCTTAGGATCAAGAGTTACTTTCGTGTTGACCGTAACAATGTTCTTCTTATTA[C/T]
TCGATTGTTGGCGAGTGGGTATCCCTTGACAGCTGGAATGCTTCATGGCACCTTATATTGGTATCTTAAAGGTGACCAATACTATTATGCTCCTAAATGT
ACATTTAGGAGCATAATAGTATTGGTCACCTTTAAGATACCAATATAAGGTGCCATGAAGCATTCCAGCTGTCAAGGGATACCCACTCGCCAACAATCGA[G/A]
TAATAAGAAGAACATTGTTACGGTCAACACGAAAGTAACTCTTGATCCTAAGACGTGGGATTGGAGGTAAATCAACACACTTATTTTGAAGCAAGGTATC
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 64.10% | 4.10% | 0.70% | 31.08% | NA |
| All Indica | 2759 | 49.20% | 1.50% | 0.76% | 48.50% | NA |
| All Japonica | 1512 | 97.50% | 1.20% | 0.13% | 1.19% | NA |
| Aus | 269 | 22.70% | 45.00% | 2.60% | 29.74% | NA |
| Indica I | 595 | 27.70% | 0.30% | 1.18% | 70.76% | NA |
| Indica II | 465 | 21.70% | 0.00% | 1.08% | 77.20% | NA |
| Indica III | 913 | 71.60% | 1.50% | 0.66% | 26.18% | NA |
| Indica Intermediate | 786 | 55.70% | 3.30% | 0.38% | 40.59% | NA |
| Temperate Japonica | 767 | 97.70% | 0.00% | 0.26% | 2.09% | NA |
| Tropical Japonica | 504 | 96.80% | 3.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.30% | 0.80% | 0.00% | 0.83% | NA |
| VI/Aromatic | 96 | 78.10% | 13.50% | 0.00% | 8.33% | NA |
| Intermediate | 90 | 66.70% | 2.20% | 3.33% | 27.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1105183588 | C -> T | LOC_Os11g09710.1 | missense_variant ; p.Thr221Ile; MODERATE | nonsynonymous_codon ; T221I | Average:13.132; most accessible tissue: Callus, score: 83.164 | unknown | unknown | DELETERIOUS | 0.00 |
| vg1105183588 | C -> DEL | LOC_Os11g09710.1 | N | frameshift_variant | Average:13.132; most accessible tissue: Callus, score: 83.164 | N | N | N | N |