| Variant ID: vg0614962408 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 14962408 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GGGTGCAGAAGGTCCGCCTACAGTTAAGAATGAAATGTTAGTACAAAACACTGATCCGGTCGCAAATAAGCACGTATGATAATAACAACTTATTTACTTA[C/T]
AGTGAACTGGAGCAACCAAGCCTTGCTAGGCCCGACTGTAGAGTACGGAGGAAGGGTGGTGGTCGGTCCTAGGTGTGGAAGGCGCATCACCTGCTCGAAG
CTTCGAGCAGGTGATGCGCCTTCCACACCTAGGACCGACCACCACCCTTCCTCCGTACTCTACAGTCGGGCCTAGCAAGGCTTGGTTGCTCCAGTTCACT[G/A]
TAAGTAAATAAGTTGTTATTATCATACGTGCTTATTTGCGACCGGATCAGTGTTTTGTACTAACATTTCATTCTTAACTGTAGGCGGACCTTCTGCACCC
| 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 | 24.80% | 0.80% | 7.68% | 66.67% | NA |
| All Indica | 2759 | 2.10% | 0.20% | 1.92% | 95.72% | NA |
| All Japonica | 1512 | 72.40% | 0.80% | 5.69% | 21.16% | NA |
| Aus | 269 | 1.10% | 5.20% | 54.28% | 39.41% | NA |
| Indica I | 595 | 4.40% | 0.00% | 1.34% | 94.29% | NA |
| Indica II | 465 | 1.10% | 0.00% | 0.65% | 98.28% | NA |
| Indica III | 913 | 0.30% | 0.10% | 2.30% | 97.26% | NA |
| Indica Intermediate | 786 | 3.20% | 0.60% | 2.67% | 93.51% | NA |
| Temperate Japonica | 767 | 90.70% | 0.70% | 4.43% | 4.17% | NA |
| Tropical Japonica | 504 | 38.50% | 1.20% | 9.13% | 51.19% | NA |
| Japonica Intermediate | 241 | 84.60% | 0.40% | 2.49% | 12.45% | NA |
| VI/Aromatic | 96 | 1.00% | 5.20% | 65.62% | 28.12% | NA |
| Intermediate | 90 | 18.90% | 1.10% | 16.67% | 63.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0614962408 | C -> T | LOC_Os06g25580.1 | N | splice_donor_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0614962408 | C -> DEL | LOC_Os06g25580.1 | N | splice_donor_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |