| Variant ID: vg0826584603 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 26584603 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CCAAATCATTGGCTCGTTGATGTACCTGGCTAGTGCAACTAGGCCTGATATCTCCTTTGCTGTGAGCAAGTTGAGCCGATTTACCTCTAATCCGGGAGAT[G/A]
ATCACTGGCGTGCACTTGAGCGAGTAATGCGCTATCTGAAAGGTACTGTGGAATTGGGGCTTCACTATACTGGGTATCCTGCGGTACTGGAGGGTTATAG
CTATAACCCTCCAGTACCGCAGGATACCCAGTATAGTGAAGCCCCAATTCCACAGTACCTTTCAGATAGCGCATTACTCGCTCAAGTGCACGCCAGTGAT[C/T]
ATCTCCCGGATTAGAGGTAAATCGGCTCAACTTGCTCACAGCAAAGGAGATATCAGGCCTAGTTGCACTAGCCAGGTACATCAACGAGCCAATGATTTGG
| 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 | 17.50% | 0.80% | 24.48% | 57.24% | NA |
| All Indica | 2759 | 8.50% | 1.40% | 32.08% | 58.06% | NA |
| All Japonica | 1512 | 31.30% | 0.00% | 9.46% | 59.26% | NA |
| Aus | 269 | 11.90% | 0.00% | 35.32% | 52.79% | NA |
| Indica I | 595 | 9.60% | 0.30% | 16.13% | 73.95% | NA |
| Indica II | 465 | 5.60% | 0.20% | 26.67% | 67.53% | NA |
| Indica III | 913 | 9.00% | 2.50% | 48.63% | 39.87% | NA |
| Indica Intermediate | 786 | 8.80% | 1.50% | 28.12% | 61.58% | NA |
| Temperate Japonica | 767 | 30.00% | 0.00% | 9.13% | 60.89% | NA |
| Tropical Japonica | 504 | 34.70% | 0.00% | 11.51% | 53.77% | NA |
| Japonica Intermediate | 241 | 28.20% | 0.00% | 6.22% | 65.56% | NA |
| VI/Aromatic | 96 | 70.80% | 0.00% | 10.42% | 18.75% | NA |
| Intermediate | 90 | 20.00% | 1.10% | 26.67% | 52.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0826584603 | G -> A | LOC_Os08g42090.1 | missense_variant ; p.Asp1116Asn; MODERATE | nonsynonymous_codon ; D1116N | Average:11.359; most accessible tissue: Minghui63 panicle, score: 20.733 | unknown | unknown | TOLERATED | 0.07 |
| vg0826584603 | G -> DEL | LOC_Os08g42090.1 | N | frameshift_variant | Average:11.359; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |