| Variant ID: vg0128724314 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 28724314 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
CATTCTTGTCCACCACGTGTCAGTTTAGCATGTCGCACGTCTGTCCTTCTTCATACAATGACTTCTTTGCAATGGTTGCGATGAAGCCTGGAATGTATCT[A/G]
GCCGGGACTGGCGTGCTAACTCCAGGAGTTAGCACACCGGCTCCGGCTAGGGACGAGTGCCTGGAGGCTCTCATCATTCCGACGGGACGGGGCGAGGCGT
ACGCCTCGCCCCGTCCCGTCGGAATGATGAGAGCCTCCAGGCACTCGTCCCTAGCCGGAGCCGGTGTGCTAACTCCTGGAGTTAGCACGCCAGTCCCGGC[T/C]
AGATACATTCCAGGCTTCATCGCAACCATTGCAAAGAAGTCATTGTATGAAGAAGGACAGACGTGCGACATGCTAAACTGACACGTGGTGGACAAGAATG
| 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 | 30.40% | 0.10% | 11.30% | 58.23% | NA |
| All Indica | 2759 | 2.30% | 0.20% | 17.11% | 80.39% | NA |
| All Japonica | 1512 | 85.40% | 0.00% | 0.13% | 14.42% | NA |
| Aus | 269 | 5.20% | 0.00% | 16.73% | 78.07% | NA |
| Indica I | 595 | 1.30% | 0.00% | 3.70% | 94.96% | NA |
| Indica II | 465 | 3.20% | 0.00% | 16.56% | 80.22% | NA |
| Indica III | 913 | 1.90% | 0.40% | 27.60% | 70.10% | NA |
| Indica Intermediate | 786 | 3.10% | 0.10% | 15.39% | 81.42% | NA |
| Temperate Japonica | 767 | 99.30% | 0.00% | 0.00% | 0.65% | NA |
| Tropical Japonica | 504 | 60.90% | 0.00% | 0.00% | 39.09% | NA |
| Japonica Intermediate | 241 | 92.50% | 0.00% | 0.83% | 6.64% | NA |
| VI/Aromatic | 96 | 21.90% | 0.00% | 9.38% | 68.75% | NA |
| Intermediate | 90 | 48.90% | 0.00% | 6.67% | 44.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0128724314 | A -> G | LOC_Os01g49990.1 | synonymous_variant ; p.Leu69Leu; LOW | synonymous_codon | Average:16.599; most accessible tissue: Zhenshan97 panicle, score: 28.447 | N | N | N | N |
| vg0128724314 | A -> DEL | LOC_Os01g49990.1 | N | frameshift_variant | Average:16.599; most accessible tissue: Zhenshan97 panicle, score: 28.447 | N | N | N | N |