| Variant ID: vg0801634797 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 1634797 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GTTCGGGCCGGCGCACCGGGAGTTCGTGTCGGTGTTCGTCAAGATGATGACCAACAGGGGCAAGGCGGCGGCGCGGTTCGACCTCCGGCTGATCGACCGC[G/A]
CCACCGGGCTGCCCCGCTCGGTGTTCCGGGCGGCGCAGCCAGTGGTGTTCGACTACTCCGTCAAGCACAAGAAGTGCAAGGGCAAGCGGGGCACCCGCGC
GCGCGGGTGCCCCGCTTGCCCTTGCACTTCTTGTGCTTGACGGAGTAGTCGAACACCACTGGCTGCGCCGCCCGGAACACCGAGCGGGGCAGCCCGGTGG[C/T]
GCGGTCGATCAGCCGGAGGTCGAACCGCGCCGCCGCCTTGCCCCTGTTGGTCATCATCTTGACGAACACCGACACGAACTCCCGGTGCGCCGGCCCGAAC
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 97.20% | 2.00% | 0.06% | 0.68% | NA |
| All Indica | 2759 | 98.30% | 0.50% | 0.07% | 1.16% | NA |
| All Japonica | 1512 | 95.00% | 4.90% | 0.07% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 96.50% | 1.20% | 0.17% | 2.18% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 98.90% | 0.20% | 0.11% | 0.77% | NA |
| Indica Intermediate | 786 | 97.80% | 0.60% | 0.00% | 1.53% | NA |
| Temperate Japonica | 767 | 94.70% | 5.20% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 93.80% | 6.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.80% | 1.20% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 95.80% | 4.20% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 96.70% | 3.30% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0801634797 | G -> A | LOC_Os08g03490.1 | missense_variant ; p.Ala99Thr; MODERATE | nonsynonymous_codon ; A99T | Average:76.827; most accessible tissue: Minghui63 flag leaf, score: 80.516 | unknown | unknown | TOLERATED | 0.35 |
| vg0801634797 | G -> DEL | LOC_Os08g03490.1 | N | frameshift_variant | Average:76.827; most accessible tissue: Minghui63 flag leaf, score: 80.516 | N | N | N | N |