| Variant ID: vg0817014807 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 17014807 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
AACCAGAACAAATTGCTTATAGAGATACTACAGCAGCATCGGATGCCAATTTTGAACCCGAGTCAGATGCAACCTCAAGTGCAGTTGGAGGCAGTCCAAG[C/T]
ACTCACACCACAAGTCAGCGCACCGCCAACATCCCAGAAGGCCCCTCATGCCATGCCACATGTTGACCCAAAAGAAGCAAGTATCATCTGTTTTATGTGT
ACACATAAAACAGATGATACTTGCTTCTTTTGGGTCAACATGTGGCATGGCATGAGGGGCCTTCTGGGATGTTGGCGGTGCGCTGACTTGTGGTGTGAGT[G/A]
CTTGGACTGCCTCCAACTGCACTTGAGGTTGCATCTGACTCGGGTTCAAAATTGGCATCCGATGCTGCTGTAGTATCTCTATAAGCAATTTGTTCTGGTT
| 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 | 19.20% | 0.10% | 30.83% | 49.83% | NA |
| All Indica | 2759 | 7.30% | 0.20% | 32.98% | 59.51% | NA |
| All Japonica | 1512 | 43.30% | 0.00% | 21.10% | 35.58% | NA |
| Aus | 269 | 8.20% | 0.00% | 50.19% | 41.64% | NA |
| Indica I | 595 | 4.90% | 0.00% | 14.79% | 80.34% | NA |
| Indica II | 465 | 3.00% | 0.00% | 27.31% | 69.68% | NA |
| Indica III | 913 | 10.80% | 0.70% | 49.07% | 39.43% | NA |
| Indica Intermediate | 786 | 7.50% | 0.00% | 31.42% | 61.07% | NA |
| Temperate Japonica | 767 | 66.80% | 0.00% | 10.82% | 22.43% | NA |
| Tropical Japonica | 504 | 11.10% | 0.00% | 32.14% | 56.75% | NA |
| Japonica Intermediate | 241 | 36.10% | 0.00% | 30.71% | 33.20% | NA |
| VI/Aromatic | 96 | 9.40% | 0.00% | 68.75% | 21.88% | NA |
| Intermediate | 90 | 23.30% | 0.00% | 30.00% | 46.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0817014807 | C -> T | LOC_Os08g27910.1 | missense_variant ; p.Ala72Val; MODERATE | nonsynonymous_codon ; A72V | Average:4.677; most accessible tissue: Minghui63 panicle, score: 7.125 | unknown | unknown | DELETERIOUS | 0.02 |
| vg0817014807 | C -> DEL | LOC_Os08g27910.1 | N | frameshift_variant | Average:4.677; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |