| Variant ID: vg0300824931 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 824931 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CGGAACGTCAAGCCTTCATCCGCGAGGAGGTGGCGCGACTTCTGGAGGCCGGATTCATCCGTGAGGTCTTCCATCCGGAGTGGCTGGCGAACCCGGTGGT[C/T]
GTTCCCAAGGCGAACGGCAAGCTTCGGATGTGCATCGACTACACCGACCTTAACAAGGCATGTCCTAAGGATCCTTACCCCCTGCCTCGCATAGATCAGA
TCTGATCTATGCGAGGCAGGGGGTAAGGATCCTTAGGACATGCCTTGTTAAGGTCGGTGTAGTCGATGCACATCCGAAGCTTGCCGTTCGCCTTGGGAAC[G/A]
ACCACCGGGTTCGCCAGCCACTCCGGATGGAAGACCTCACGGATGAATCCGGCCTCCAGAAGTCGCGCCACCTCCTCGCGGATGAAGGCTTGACGTTCCG
| 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 | 13.60% | 0.10% | 1.46% | 84.81% | NA |
| All Indica | 2759 | 1.30% | 0.00% | 0.11% | 98.62% | NA |
| All Japonica | 1512 | 37.30% | 0.00% | 0.33% | 62.37% | NA |
| Aus | 269 | 6.30% | 1.90% | 17.10% | 74.72% | NA |
| Indica I | 595 | 0.70% | 0.00% | 0.00% | 99.33% | NA |
| Indica II | 465 | 4.10% | 0.00% | 0.00% | 95.91% | NA |
| Indica III | 913 | 0.80% | 0.00% | 0.22% | 99.01% | NA |
| Indica Intermediate | 786 | 0.60% | 0.00% | 0.13% | 99.24% | NA |
| Temperate Japonica | 767 | 60.60% | 0.00% | 0.52% | 38.85% | NA |
| Tropical Japonica | 504 | 6.30% | 0.00% | 0.20% | 93.45% | NA |
| Japonica Intermediate | 241 | 27.80% | 0.00% | 0.00% | 72.20% | NA |
| VI/Aromatic | 96 | 11.50% | 0.00% | 14.58% | 73.96% | NA |
| Intermediate | 90 | 18.90% | 0.00% | 1.11% | 80.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0300824931 | C -> T | LOC_Os03g02350.1 | synonymous_variant ; p.Val870Val; LOW | synonymous_codon | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0300824931 | C -> DEL | LOC_Os03g02350.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |