| Variant ID: vg1105182696 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 5182696 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
AATCCCATCGTTTTCTCGTTTACTACCGGCATTTTTTCATTGGTACTTTTTCTTTTTTTAGATCTGAAATGTCCTCGAGTGAAGGATCTAAGTGGGTTTC[G/A]
CGATGTGTCTTTGGCTCCCCTCCGAATCTTTCTGAGCTAGATGAGTTGGCGGTTCTTTATCATGAACAAGCTGCAAGGAACACTAGAGACTACGTTAGAA
TTCTAACGTAGTCTCTAGTGTTCCTTGCAGCTTGTTCATGATAAAGAACCGCCAACTCATCTAGCTCAGAAAGATTCGGAGGGGAGCCAAAGACACATCG[C/T]
GAAACCCACTTAGATCCTTCACTCGAGGACATTTCAGATCTAAAAAAAGAAAAAGTACCAATGAAAAAATGCCGGTAGTAAACGAGAAAACGATGGGATT
| 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 | 64.60% | 3.60% | 0.76% | 31.00% | NA |
| All Indica | 2759 | 44.70% | 6.10% | 1.16% | 48.10% | NA |
| All Japonica | 1512 | 98.80% | 0.00% | 0.00% | 1.19% | NA |
| Aus | 269 | 66.50% | 0.00% | 0.74% | 32.71% | NA |
| Indica I | 595 | 13.80% | 14.10% | 1.34% | 70.76% | NA |
| Indica II | 465 | 21.10% | 1.30% | 1.94% | 75.70% | NA |
| Indica III | 913 | 70.30% | 3.00% | 0.99% | 25.74% | NA |
| Indica Intermediate | 786 | 52.30% | 6.40% | 0.76% | 40.59% | NA |
| Temperate Japonica | 767 | 97.90% | 0.00% | 0.00% | 2.09% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.00% | 0.00% | 0.83% | NA |
| VI/Aromatic | 96 | 90.60% | 0.00% | 0.00% | 9.38% | NA |
| Intermediate | 90 | 67.80% | 4.40% | 2.22% | 25.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1105182696 | G -> A | LOC_Os11g09710.1 | synonymous_variant ; p.Ser11Ser; LOW | synonymous_codon | Average:14.345; most accessible tissue: Callus, score: 85.245 | N | N | N | N |
| vg1105182696 | G -> DEL | LOC_Os11g09710.1 | N | frameshift_variant | Average:14.345; most accessible tissue: Callus, score: 85.245 | N | N | N | N |