| Variant ID: vg1209004531 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 9004531 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
TGCCCAACAACGGTGGTGTGACCAACCAACCGTGTAGGCGAGGACACTAGTTGACAGTGGACGAGGCGGCCGGTCAGTGAAGACGATGATGTCCATCAGC[A/G]
GCGGCGCAATATGCCAGCCGTGAAGGCGAAGAGGCTTGTCGACGGAAGATGAGGCAGCTGGCAGTGTAGAATATGTCATTATCAGCCATGGCGATAAAGA
TCTTTATCGCCATGGCTGATAATGACATATTCTACACTGCCAGCTGCCTCATCTTCCGTCGACAAGCCTCTTCGCCTTCACGGCTGGCATATTGCGCCGC[T/C]
GCTGATGGACATCATCGTCTTCACTGACCGGCCGCCTCGTCCACTGTCAACTAGTGTCCTCGCCTACACGGTTGGTTGGTCACACCACCGTTGTTGGGCA
| 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 | 78.60% | 0.40% | 0.44% | 20.63% | NA |
| All Indica | 2759 | 65.50% | 0.60% | 0.72% | 33.20% | NA |
| All Japonica | 1512 | 99.10% | 0.00% | 0.00% | 0.93% | NA |
| Aus | 269 | 87.40% | 0.00% | 0.37% | 12.27% | NA |
| Indica I | 595 | 59.20% | 0.20% | 0.84% | 39.83% | NA |
| Indica II | 465 | 67.10% | 0.00% | 0.22% | 32.69% | NA |
| Indica III | 913 | 66.70% | 1.30% | 0.66% | 31.33% | NA |
| Indica Intermediate | 786 | 67.80% | 0.50% | 1.02% | 30.66% | NA |
| Temperate Japonica | 767 | 99.20% | 0.00% | 0.00% | 0.78% | NA |
| Tropical Japonica | 504 | 99.20% | 0.00% | 0.00% | 0.79% | NA |
| Japonica Intermediate | 241 | 98.30% | 0.00% | 0.00% | 1.66% | NA |
| VI/Aromatic | 96 | 95.80% | 0.00% | 0.00% | 4.17% | NA |
| Intermediate | 90 | 91.10% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1209004531 | A -> DEL | LOC_Os12g15770.1 | N | frameshift_variant | Average:45.395; most accessible tissue: Callus, score: 82.589 | N | N | N | N |
| vg1209004531 | A -> G | LOC_Os12g15770.1 | missense_variant ; p.Leu36Pro; MODERATE | nonsynonymous_codon ; L36P | Average:45.395; most accessible tissue: Callus, score: 82.589 | unknown | unknown | TOLERATED | 1.00 |