| Variant ID: vg0143001172 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 43001172 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CAATCACCTCCCTGGGGACCCCGGGCATATCCGCCGGTCTCCATGCGAAGACGTCAGCGTTTGCCCGTAGGAAGGAGACGAGCGCGTCTTCCTATTTGCC[G/A]
TCCAAAAGACCACCGATCCGTGTGGTCTTGGACGGGCCGTCGCCCAGGGCAACCTCCTTGACCGGGACCTCGTCGCCTGTGATCATCCGCTGCCTCGGGG
CCCCGAGGCAGCGGATGATCACAGGCGACGAGGTCCCGGTCAAGGAGGTTGCCCTGGGCGACGGCCCGTCCAAGACCACACGGATCGGTGGTCTTTTGGA[C/T]
GGCAAATAGGAAGACGCGCTCGTCTCCTTCCTACGGGCAAACGCTGACGTCTTCGCATGGAGACCGGCGGATATGCCCGGGGTCCCCAGGGAGGTGATTG
| 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 | 7.00% | 0.10% | 2.86% | 90.01% | NA |
| All Indica | 2759 | 0.50% | 0.00% | 1.20% | 98.26% | NA |
| All Japonica | 1512 | 20.20% | 0.00% | 0.46% | 79.37% | NA |
| Aus | 269 | 0.70% | 1.50% | 35.32% | 62.45% | NA |
| Indica I | 595 | 0.50% | 0.00% | 0.17% | 99.33% | NA |
| Indica II | 465 | 0.90% | 0.00% | 0.22% | 98.92% | NA |
| Indica III | 913 | 0.10% | 0.10% | 1.64% | 98.14% | NA |
| Indica Intermediate | 786 | 0.80% | 0.00% | 2.04% | 97.20% | NA |
| Temperate Japonica | 767 | 37.90% | 0.00% | 0.65% | 61.41% | NA |
| Tropical Japonica | 504 | 1.20% | 0.00% | 0.40% | 98.41% | NA |
| Japonica Intermediate | 241 | 3.30% | 0.00% | 0.00% | 96.68% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 0.00% | 100.00% | NA |
| Intermediate | 90 | 12.20% | 0.00% | 0.00% | 87.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0143001172 | G -> A | LOC_Os01g74220.1 | downstream_gene_variant ; 4368.0bp to feature; MODIFIER | silent_mutation | Average:12.962; most accessible tissue: Minghui63 young leaf, score: 28.65 | N | N | N | N |
| vg0143001172 | G -> A | LOC_Os01g74230.1 | intron_variant ; MODIFIER | silent_mutation | Average:12.962; most accessible tissue: Minghui63 young leaf, score: 28.65 | N | N | N | N |
| vg0143001172 | G -> DEL | N | N | silent_mutation | Average:12.962; most accessible tissue: Minghui63 young leaf, score: 28.65 | N | N | N | N |