| Variant ID: vg0324794507 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 24794507 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TGCCCTCGATGGCGGACCTGCCGCACGCCTCCGCCTAGCGGAGCCCAACCTGCGCGCCAGATGGATGCTGTGCTTGGTTGTTGCGTGCTGCTAGTTGTTG[G/A]
GCCGGCGTCCCCAGCGGAAGCCACATACGCGACTGAGCCGGCGAGCCTCGCCTCCGCCTTGCACCCCCAGCGGCCGGCTCAAGCTGCTGTCTATCTCTAT
ATAGAGATAGACAGCAGCTTGAGCCGGCCGCTGGGGGTGCAAGGCGGAGGCGAGGCTCGCCGGCTCAGTCGCGTATGTGGCTTCCGCTGGGGACGCCGGC[C/T]
CAACAACTAGCAGCACGCAACAACCAAGCACAGCATCCATCTGGCGCGCAGGTTGGGCTCCGCTAGGCGGAGGCGTGCGGCAGGTCCGCCATCGAGGGCA
| 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 | 62.40% | 0.20% | 8.27% | 29.09% | NA |
| All Indica | 2759 | 39.40% | 0.00% | 12.14% | 48.46% | NA |
| All Japonica | 1512 | 98.80% | 0.60% | 0.07% | 0.53% | NA |
| Aus | 269 | 80.30% | 0.00% | 17.84% | 1.86% | NA |
| Indica I | 595 | 73.40% | 0.00% | 4.54% | 22.02% | NA |
| Indica II | 465 | 11.60% | 0.00% | 5.59% | 82.80% | NA |
| Indica III | 913 | 25.20% | 0.00% | 21.69% | 53.12% | NA |
| Indica Intermediate | 786 | 46.60% | 0.00% | 10.69% | 42.75% | NA |
| Temperate Japonica | 767 | 98.20% | 1.20% | 0.13% | 0.52% | NA |
| Tropical Japonica | 504 | 99.20% | 0.00% | 0.00% | 0.79% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 94.80% | 0.00% | 3.12% | 2.08% | NA |
| Intermediate | 90 | 70.00% | 0.00% | 4.44% | 25.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0324794507 | G -> A | LOC_Os03g44130.1 | 5_prime_UTR_variant ; 325.0bp to feature; MODIFIER | silent_mutation | Average:22.568; most accessible tissue: Zhenshan97 flag leaf, score: 57.42 | N | N | N | N |
| vg0324794507 | G -> A | LOC_Os03g44140.1 | downstream_gene_variant ; 3297.0bp to feature; MODIFIER | silent_mutation | Average:22.568; most accessible tissue: Zhenshan97 flag leaf, score: 57.42 | N | N | N | N |
| vg0324794507 | G -> DEL | N | N | silent_mutation | Average:22.568; most accessible tissue: Zhenshan97 flag leaf, score: 57.42 | N | N | N | N |