| Variant ID: vg1114174000 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 14174000 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TGCAACACTCTTCATTGGTAGCTCCTTACATCGAGGAGCACTTGGCTCTAGTTCGCGCAAGGAACATCGGTAAGTCCGATGCATGGATTACACGACATCA[C/T]
ATTGATACTTTCCCCGCGTGGCTACGACAACATCTCATGGGTAACGAGTCGATCAACCAACAACTTGCCTTCCTGGCGAGGGGACCGTCTGGGTCGATCG
CGATCGACCCAGACGGTCCCCTCGCCAGGAAGGCAAGTTGTTGGTTGATCGACTCGTTACCCATGAGATGTTGTCGTAGCCACGCGGGGAAAGTATCAAT[G/A]
TGATGTCGTGTAATCCATGCATCGGACTTACCGATGTTCCTTGCGCGAACTAGAGCCAAGTGCTCCTCGATGTAAGGAGCTACCAATGAAGAGTGTTGCA
| 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 | 34.70% | 0.40% | 3.39% | 61.51% | NA |
| All Indica | 2759 | 2.70% | 0.00% | 5.33% | 91.92% | NA |
| All Japonica | 1512 | 96.60% | 0.10% | 0.40% | 2.98% | NA |
| Aus | 269 | 0.70% | 0.00% | 1.49% | 97.77% | NA |
| Indica I | 595 | 3.40% | 0.00% | 3.70% | 92.94% | NA |
| Indica II | 465 | 1.70% | 0.00% | 4.95% | 93.33% | NA |
| Indica III | 913 | 1.30% | 0.00% | 5.70% | 92.99% | NA |
| Indica Intermediate | 786 | 4.50% | 0.10% | 6.36% | 89.06% | NA |
| Temperate Japonica | 767 | 96.30% | 0.00% | 0.39% | 3.26% | NA |
| Tropical Japonica | 504 | 96.40% | 0.00% | 0.60% | 2.98% | NA |
| Japonica Intermediate | 241 | 97.50% | 0.40% | 0.00% | 2.07% | NA |
| VI/Aromatic | 96 | 70.80% | 15.60% | 1.04% | 12.50% | NA |
| Intermediate | 90 | 41.10% | 0.00% | 2.22% | 56.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1114174000 | C -> T | LOC_Os11g24860.1 | synonymous_variant ; p.His877His; LOW | synonymous_codon | Average:4.721; most accessible tissue: Callus, score: 7.257 | N | N | N | N |
| vg1114174000 | C -> DEL | LOC_Os11g24860.1 | N | frameshift_variant | Average:4.721; most accessible tissue: Callus, score: 7.257 | N | N | N | N |