| Variant ID: vg0329361717 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 29361717 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
ACCCGTCCAACACCGTGGTGTTTGCGATGGCCAAGGCCTGCAGAAGGGGTTCTGCGCTCAGTGGAGCAACGGAAGGCGTGGGGAAGAGCCGCCTCGAAGA[G/A]
GATGCTGCGCGGCTTGGCCCGCCGATGGACGTGCCGGACTCGGGGATGTCCCCCGGACCTGGTTTGTCCTGAGCGTCGCACGAGGGAGTGGGCCCAAGCG
CGCTTGGGCCCACTCCCTCGTGCGACGCTCAGGACAAACCAGGTCCGGGGGACATCCCCGAGTCCGGCACGTCCATCGGCGGGCCAAGCCGCGCAGCATC[C/T]
TCTTCGAGGCGGCTCTTCCCCACGCCTTCCGTTGCTCCACTGAGCGCAGAACCCCTTCTGCAGGCCTTGGCCATCGCAAACACCACGGTGTTGGACGGGT
| 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 | 56.20% | 0.10% | 0.57% | 43.14% | NA |
| All Indica | 2759 | 37.70% | 0.20% | 0.22% | 61.83% | NA |
| All Japonica | 1512 | 99.50% | 0.00% | 0.07% | 0.46% | NA |
| Aus | 269 | 0.40% | 0.00% | 0.00% | 99.63% | NA |
| Indica I | 595 | 53.10% | 0.00% | 0.00% | 46.89% | NA |
| Indica II | 465 | 37.80% | 0.20% | 0.00% | 61.94% | NA |
| Indica III | 913 | 28.50% | 0.20% | 0.33% | 70.97% | NA |
| Indica Intermediate | 786 | 36.80% | 0.40% | 0.38% | 62.47% | NA |
| Temperate Japonica | 767 | 99.60% | 0.00% | 0.00% | 0.39% | NA |
| Tropical Japonica | 504 | 99.40% | 0.00% | 0.00% | 0.60% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.00% | 0.41% | 0.41% | NA |
| VI/Aromatic | 96 | 52.10% | 0.00% | 18.75% | 29.17% | NA |
| Intermediate | 90 | 64.40% | 0.00% | 2.22% | 33.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0329361717 | G -> A | LOC_Os03g51320.1 | synonymous_variant ; p.Ser549Ser; LOW | synonymous_codon | Average:35.377; most accessible tissue: Zhenshan97 flag leaf, score: 75.761 | N | N | N | N |
| vg0329361717 | G -> DEL | LOC_Os03g51320.1 | N | frameshift_variant | Average:35.377; most accessible tissue: Zhenshan97 flag leaf, score: 75.761 | N | N | N | N |