| Variant ID: vg0143001655 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 43001655 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
AGGTGACCGGTAGGTCGATGTGACCTAACGGCCACGTGTGCCCCGGCGTCACACCGATAATTGGCTGGGACGGCCGGAGCACCATCCCCGGGGCCTTGAT[G/A]
GCGTCAAAGGCCGCAGGGGAAAGGATGTTGAGGGCCACTCCCCCATCAATGAGGACACGCTCCAACTTCACGTTGCAAACGGTGGGAGAAACCACCATCG
CGATGGTGGTTTCTCCCACCGTTTGCAACGTGAAGTTGGAGCGTGTCCTCATTGATGGGGGAGTGGCCCTCAACATCCTTTCCCCTGCGGCCTTTGACGC[C/T]
ATCAAGGCCCCGGGGATGGTGCTCCGGCCGTCCCAGCCAATTATCGGTGTGACGCCGGGGCACACGTGGCCGTTAGGTCACATCGACCTACCGGTCACCT
| 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 | 8.40% | 0.40% | 3.72% | 87.52% | NA |
| All Indica | 2759 | 2.10% | 0.70% | 5.44% | 91.74% | NA |
| All Japonica | 1512 | 20.80% | 0.00% | 0.73% | 78.44% | NA |
| Aus | 269 | 1.50% | 0.00% | 3.35% | 95.17% | NA |
| Indica I | 595 | 1.30% | 1.70% | 1.34% | 95.63% | NA |
| Indica II | 465 | 0.60% | 0.00% | 2.80% | 96.56% | NA |
| Indica III | 913 | 2.60% | 0.10% | 8.43% | 88.83% | NA |
| Indica Intermediate | 786 | 3.10% | 1.00% | 6.62% | 89.31% | NA |
| Temperate Japonica | 767 | 39.10% | 0.00% | 0.26% | 60.63% | NA |
| Tropical Japonica | 504 | 1.20% | 0.00% | 1.59% | 97.22% | NA |
| Japonica Intermediate | 241 | 3.70% | 0.00% | 0.41% | 95.85% | NA |
| VI/Aromatic | 96 | 3.10% | 0.00% | 3.12% | 93.75% | NA |
| Intermediate | 90 | 15.60% | 0.00% | 3.33% | 81.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0143001655 | G -> A | LOC_Os01g74230.1 | synonymous_variant ; p.Ala473Ala; LOW | synonymous_codon | Average:16.119; most accessible tissue: Zhenshan97 panicle, score: 39.652 | N | N | N | N |
| vg0143001655 | G -> DEL | LOC_Os01g74230.1 | N | frameshift_variant | Average:16.119; most accessible tissue: Zhenshan97 panicle, score: 39.652 | N | N | N | N |