| Variant ID: vg0314254436 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 14254436 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TGCAAATTGGAACGAATCAATACTTTTTGATCCTTGTGAGGCTATTTCAGCACATTTCCTTGACAGAATATTGAATCTGAGGACTGAGCTCTCCGATAAA[G/T]
GTATAATTCTATCTTCAAAATCATATTTTTCTTTGTAATCCTTTTTTCTCCACCGATCAATAATATATTTCTTTGGAATCTTCATAATGTTGAGGTGAAG
CTTCACCTCAACATTATGAAGATTCCAAAGAAATATATTATTGATCGGTGGAGAAAAAAGGATTACAAAGAAAAATATGATTTTGAAGATAGAATTATAC[C/A]
TTTATCGGAGAGCTCAGTCCTCAGATTCAATATTCTGTCAAGGAAATGTGCTGAAATAGCCTCACAAGGATCAAAAAGTATTGATTCGTTCCAATTTGCA
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 70.10% | 28.90% | 0.78% | 0.30% | NA |
| All Indica | 2759 | 54.20% | 44.30% | 1.12% | 0.43% | NA |
| All Japonica | 1512 | 99.70% | 0.30% | 0.07% | 0.00% | NA |
| Aus | 269 | 56.90% | 41.60% | 0.74% | 0.74% | NA |
| Indica I | 595 | 80.30% | 18.70% | 0.67% | 0.34% | NA |
| Indica II | 465 | 63.20% | 34.80% | 1.29% | 0.65% | NA |
| Indica III | 913 | 36.70% | 62.00% | 1.10% | 0.22% | NA |
| Indica Intermediate | 786 | 49.20% | 48.70% | 1.40% | 0.64% | NA |
| Temperate Japonica | 767 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.20% | 0.60% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 87.50% | 12.50% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 81.10% | 15.60% | 3.33% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0314254436 | G -> T | LOC_Os03g24970.1 | missense_variant ; p.Pro150His; MODERATE | nonsynonymous_codon ; P150H | Average:4.462; most accessible tissue: Minghui63 panicle, score: 7.125 | unknown | unknown | DELETERIOUS | 0.01 |
| vg0314254436 | G -> DEL | LOC_Os03g24970.1 | N | frameshift_variant | Average:4.462; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |