| Variant ID: vg0904848203 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 4848203 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
GCATAGTGCCCTTGCTCATCACACATAAAACAGATGATACTTGCTTCTTTTGGGTCAACATGTGGCATGGCATGAGGGGCCTTCTGGGATGTTGGCGGTG[T/C]
GCTGACTTGTGGTGTGAGTGCTTGGACTGCCTCCAACTGCACTTGAGGTTGTATTTGACTCAAGTTCAGAATTGGCGTCTGGTGCTGCTGTAGTATCTCT
AGAGATACTACAGCAGCACCAGACGCCAATTCTGAACTTGAGTCAAATACAACCTCAAGTGCAGTTGGAGGCAGTCCAAGCACTCACACCACAAGTCAGC[A/G]
CACCGCCAACATCCCAGAAGGCCCCTCATGCCATGCCACATGTTGACCCAAAAGAAGCAAGTATCATCTGTTTTATGTGTGATGAGCAAGGGCACTATGC
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 14.00% | 0.20% | 1.69% | 84.15% | NA |
| All Indica | 2759 | 2.90% | 0.10% | 0.51% | 96.45% | NA |
| All Japonica | 1512 | 30.90% | 0.30% | 2.98% | 65.87% | NA |
| Aus | 269 | 17.10% | 0.00% | 2.23% | 80.67% | NA |
| Indica I | 595 | 5.50% | 0.00% | 0.00% | 94.45% | NA |
| Indica II | 465 | 3.70% | 0.00% | 0.22% | 96.13% | NA |
| Indica III | 913 | 0.50% | 0.20% | 0.44% | 98.80% | NA |
| Indica Intermediate | 786 | 3.20% | 0.30% | 1.15% | 95.42% | NA |
| Temperate Japonica | 767 | 38.70% | 0.10% | 1.04% | 60.10% | NA |
| Tropical Japonica | 504 | 20.20% | 0.20% | 2.78% | 76.79% | NA |
| Japonica Intermediate | 241 | 28.20% | 0.80% | 9.54% | 61.41% | NA |
| VI/Aromatic | 96 | 53.10% | 0.00% | 11.46% | 35.42% | NA |
| Intermediate | 90 | 18.90% | 0.00% | 4.44% | 76.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0904848203 | T -> DEL | LOC_Os09g09070.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0904848203 | T -> C | LOC_Os09g09070.1 | missense_variant ; p.Thr79Ala; MODERATE | nonsynonymous_codon ; T79A | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | unknown | unknown | TOLERATED | 1.00 |