| Variant ID: vg1209004619 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 9004619 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
ATGTCCATCAGCAGCGGCGCAATATGCCAGCCGTGAAGGCGAAGAGGCTTGTCGACGGAAGATGAGGCAGCTGGCAGTGTAGAATATGTCATTATCAGCC[A/G]
TGGCGATAAAGACAACATGTTTGGATAAATCCAATACACGGTATGGTAGGCGGAGCCTGCAGCTTGATTAATGTCATCGGCTGTCACCACAGCATTTGAT
ATCAAATGCTGTGGTGACAGCCGATGACATTAATCAAGCTGCAGGCTCCGCCTACCATACCGTGTATTGGATTTATCCAAACATGTTGTCTTTATCGCCA[T/C]
GGCTGATAATGACATATTCTACACTGCCAGCTGCCTCATCTTCCGTCGACAAGCCTCTTCGCCTTCACGGCTGGCATATTGCGCCGCTGCTGATGGACAT
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 68.60% | 10.00% | 0.49% | 20.97% | NA |
| All Indica | 2759 | 59.50% | 6.20% | 0.69% | 33.67% | NA |
| All Japonica | 1512 | 98.50% | 0.40% | 0.13% | 0.93% | NA |
| Aus | 269 | 6.30% | 80.30% | 0.00% | 13.38% | NA |
| Indica I | 595 | 52.90% | 5.50% | 1.01% | 40.50% | NA |
| Indica II | 465 | 64.70% | 1.30% | 1.08% | 32.90% | NA |
| Indica III | 913 | 61.20% | 6.70% | 0.44% | 31.65% | NA |
| Indica Intermediate | 786 | 59.30% | 8.90% | 0.51% | 31.30% | NA |
| Temperate Japonica | 767 | 98.70% | 0.30% | 0.26% | 0.78% | NA |
| Tropical Japonica | 504 | 99.00% | 0.20% | 0.00% | 0.79% | NA |
| Japonica Intermediate | 241 | 97.10% | 1.20% | 0.00% | 1.66% | NA |
| VI/Aromatic | 96 | 26.00% | 67.70% | 2.08% | 4.17% | NA |
| Intermediate | 90 | 75.60% | 15.60% | 0.00% | 8.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1209004619 | A -> DEL | LOC_Os12g15770.1 | N | frameshift_variant | Average:45.713; most accessible tissue: Minghui63 flag leaf, score: 76.091 | N | N | N | N |
| vg1209004619 | A -> G | LOC_Os12g15770.1 | missense_variant ; p.Trp7Arg; MODERATE | nonsynonymous_codon ; W7R | Average:45.713; most accessible tissue: Minghui63 flag leaf, score: 76.091 | unknown | unknown | TOLERATED | 0.24 |