| Variant ID: vg0128724293 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 28724293 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TCAGACCAGTCACAGACCGGTCATTCTTGTCCACCACGTGTCAGTTTAGCATGTCGCACGTCTGTCCTTCTTCATACAATGACTTCTTTGCAATGGTTGC[G/A]
ATGAAGCCTGGAATGTATCTAGCCGGGACTGGCGTGCTAACTCCAGGAGTTAGCACACCGGCTCCGGCTAGGGACGAGTGCCTGGAGGCTCTCATCATTC
GAATGATGAGAGCCTCCAGGCACTCGTCCCTAGCCGGAGCCGGTGTGCTAACTCCTGGAGTTAGCACGCCAGTCCCGGCTAGATACATTCCAGGCTTCAT[C/T]
GCAACCATTGCAAAGAAGTCATTGTATGAAGAAGGACAGACGTGCGACATGCTAAACTGACACGTGGTGGACAAGAATGACCGGTCTGTGACTGGTCTGA
| 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 | 32.50% | 3.90% | 16.38% | 47.25% | NA |
| All Indica | 2759 | 5.50% | 6.60% | 25.59% | 62.31% | NA |
| All Japonica | 1512 | 85.40% | 0.00% | 0.46% | 14.09% | NA |
| Aus | 269 | 7.80% | 0.00% | 14.13% | 78.07% | NA |
| Indica I | 595 | 2.00% | 2.50% | 16.64% | 78.82% | NA |
| Indica II | 465 | 3.40% | 3.40% | 20.65% | 72.47% | NA |
| Indica III | 913 | 7.70% | 11.80% | 34.94% | 45.56% | NA |
| Indica Intermediate | 786 | 7.00% | 5.30% | 24.43% | 63.23% | NA |
| Temperate Japonica | 767 | 99.30% | 0.00% | 0.00% | 0.65% | NA |
| Tropical Japonica | 504 | 60.90% | 0.00% | 0.60% | 38.49% | NA |
| Japonica Intermediate | 241 | 92.50% | 0.00% | 1.66% | 5.81% | NA |
| VI/Aromatic | 96 | 25.00% | 0.00% | 15.62% | 59.38% | NA |
| Intermediate | 90 | 51.10% | 2.20% | 8.89% | 37.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0128724293 | G -> A | LOC_Os01g49990.1 | synonymous_variant ; p.Ala62Ala; LOW | synonymous_codon | Average:14.853; most accessible tissue: Zhenshan97 panicle, score: 24.575 | N | N | N | N |
| vg0128724293 | G -> DEL | LOC_Os01g49990.1 | N | frameshift_variant | Average:14.853; most accessible tissue: Zhenshan97 panicle, score: 24.575 | N | N | N | N |