| Variant ID: vg1115080661 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 15080661 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
ACATGACACAACAAAGAAGGCTCGAAGCATTCAGAACAACACAGTTGTGAAAGCACTTTTTAACGGCGCTAATTTGCAAGGAACAACAAGTACTACCCGG[C/A]
AAAATATTTCTTCACAACATCTTAGGAATGTTGCTAGAAATTTTGTACGGTCCCGAACTGATCAGGTAATTACAAATCTTCAGCAAGCTGCTATGTTGAA
TTCAACATAGCAGCTTGCTGAAGATTTGTAATTACCTGATCAGTTCGGGACCGTACAAAATTTCTAGCAACATTCCTAAGATGTTGTGAAGAAATATTTT[G/T]
CCGGGTAGTACTTGTTGTTCCTTGCAAATTAGCGCCGTTAAAAAGTGCTTTCACAACTGTGTTGTTCTGAATGCTTCGAGCCTTCTTTGTTGTGTCATGT
| 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 | 53.60% | 0.20% | 24.55% | 21.63% | NA |
| All Indica | 2759 | 23.60% | 0.00% | 40.85% | 35.52% | NA |
| All Japonica | 1512 | 97.40% | 0.70% | 0.73% | 1.26% | NA |
| Aus | 269 | 94.80% | 0.00% | 1.12% | 4.09% | NA |
| Indica I | 595 | 20.30% | 0.00% | 25.21% | 54.45% | NA |
| Indica II | 465 | 11.00% | 0.00% | 58.71% | 30.32% | NA |
| Indica III | 913 | 29.90% | 0.00% | 42.17% | 27.93% | NA |
| Indica Intermediate | 786 | 26.30% | 0.00% | 40.59% | 33.08% | NA |
| Temperate Japonica | 767 | 98.30% | 0.00% | 0.26% | 1.43% | NA |
| Tropical Japonica | 504 | 95.80% | 2.00% | 1.59% | 0.60% | NA |
| Japonica Intermediate | 241 | 97.50% | 0.00% | 0.41% | 2.07% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 65.60% | 0.00% | 21.11% | 13.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1115080661 | C -> A | LOC_Os11g26350.1 | missense_variant ; p.Gln160Lys; MODERATE | nonsynonymous_codon ; Q160K | Average:4.664; most accessible tissue: Minghui63 panicle, score: 7.125 | unknown | unknown | DELETERIOUS | 0.00 |
| vg1115080661 | C -> DEL | LOC_Os11g26350.1 | N | frameshift_variant | Average:4.664; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |