| Variant ID: vg0300825672 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 825672 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
AGCTTCTCAAACGCTCCGGACCGTTTACCTGGACGGAGGAAGCCGAAAATGCCCTCACTCAGTTGAAGGCATGTCTAAGCTCTCCCCCAGTTCTGGTCGC[C/T]
CCGGAGCCAGACGAGCCCTTGTTACTCTACTTAGCGGCGACCCCGCAAGTAGTTAGTGCGGCATTGGTTGTGGAGCGCGATGAGGACAATTCTCATTTCA
TGAAATGAGAATTGTCCTCATCGCGCTCCACAACCAATGCCGCACTAACTACTTGCGGGGTCGCCGCTAAGTAGAGTAACAAGGGCTCGTCTGGCTCCGG[G/A]
GCGACCAGAACTGGGGGAGAGCTTAGACATGCCTTCAACTGAGTGAGGGCATTTTCGGCTTCCTCCGTCCAGGTAAACGGTCCGGAGCGTTTGAGAAGCT
| 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 | 13.10% | 0.20% | 0.89% | 85.84% | NA |
| All Indica | 2759 | 1.20% | 0.30% | 1.34% | 97.14% | NA |
| All Japonica | 1512 | 37.10% | 0.10% | 0.20% | 62.63% | NA |
| Aus | 269 | 1.50% | 0.00% | 0.37% | 98.14% | NA |
| Indica I | 595 | 0.50% | 0.20% | 1.18% | 98.15% | NA |
| Indica II | 465 | 4.50% | 0.20% | 2.80% | 92.47% | NA |
| Indica III | 913 | 0.40% | 0.20% | 0.55% | 98.80% | NA |
| Indica Intermediate | 786 | 0.80% | 0.50% | 1.53% | 97.20% | NA |
| Temperate Japonica | 767 | 60.90% | 0.00% | 0.13% | 38.98% | NA |
| Tropical Japonica | 504 | 6.00% | 0.20% | 0.20% | 93.65% | NA |
| Japonica Intermediate | 241 | 26.60% | 0.00% | 0.41% | 73.03% | NA |
| VI/Aromatic | 96 | 5.20% | 0.00% | 0.00% | 94.79% | NA |
| Intermediate | 90 | 15.60% | 0.00% | 1.11% | 83.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0300825672 | C -> T | LOC_Os03g02350.1 | synonymous_variant ; p.Ala1117Ala; LOW | synonymous_codon | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0300825672 | C -> DEL | LOC_Os03g02350.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |