| Variant ID: vg0108457594 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 8457594 |
| Reference Allele: G | Alternative Allele: A,T |
| Primary Allele: G | Secondary Allele: Unkown |
Inferred Ancestral Allele: Not determined.
ACGCCAAGACACGCCGCCGGATATCGACTTGAAGGATAGGCATGGCTATTCCCCTACGGTGTCTCCGGATACCGTCAGGAGATACGAAAGCGCTATCTCT[G/A,T]
ATCTCGCCGGGCACAGATTCGAGGAGGAAGACTACCCTGTTGTCGACTACGAGTCAGACCTTCAGACCGACATGTCCACAACAGTTAGATAGGCTACCCA
TGGGTAGCCTATCTAACTGTTGTGGACATGTCGGTCTGAAGGTCTGACTCGTAGTCGACAACAGGGTAGTCTTCCTCCTCGAATCTGTGCCCGGCGAGAT[C/T,A]
AGAGATAGCGCTTTCGTATCTCCTGACGGTATCCGGAGACACCGTAGGGGAATAGCCATGCCTATCCTTCAAGTCGATATCCGGCGGCGTGTCTTGGCGT
| Populations | Population Size | Frequency of G(primary allele) | Frequency of Unkown(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 73.60% | 0.00% | 3.41% | 23.02% | NA |
| All Indica | 2759 | 65.30% | 0.00% | 3.59% | 31.13% | NA |
| All Japonica | 1512 | 86.70% | 0.00% | 2.05% | 11.24% | NA |
| Aus | 269 | 73.60% | 0.00% | 10.04% | 16.36% | NA |
| Indica I | 595 | 76.00% | 0.00% | 3.19% | 20.84% | NA |
| Indica II | 465 | 66.20% | 0.00% | 1.94% | 31.83% | NA |
| Indica III | 913 | 55.60% | 0.00% | 4.82% | 39.54% | NA |
| Indica Intermediate | 786 | 67.80% | 0.00% | 3.44% | 28.75% | NA |
| Temperate Japonica | 767 | 97.70% | 0.00% | 0.39% | 1.96% | NA |
| Tropical Japonica | 504 | 68.80% | 0.00% | 4.37% | 26.79% | NA |
| Japonica Intermediate | 241 | 89.20% | 0.00% | 2.49% | 8.30% | NA |
| VI/Aromatic | 96 | 95.80% | 0.00% | 2.08% | 2.08% | NA |
| Intermediate | 90 | 83.30% | 0.00% | 2.22% | 14.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0108457594 | G -> T | LOC_Os01g15070.1 | missense_variant ; p.Asp57Tyr; MODERATE | N | Average:55.996; most accessible tissue: Minghui63 young leaf, score: 70.038 | N | N | N | N |
| vg0108457594 | G -> T | LOC_Os01g15080.1 | upstream_gene_variant ; 365.0bp to feature; MODIFIER | N | Average:55.996; most accessible tissue: Minghui63 young leaf, score: 70.038 | N | N | N | N |
| vg0108457594 | G -> T | LOC_Os01g15090.1 | upstream_gene_variant ; 3478.0bp to feature; MODIFIER | N | Average:55.996; most accessible tissue: Minghui63 young leaf, score: 70.038 | N | N | N | N |
| vg0108457594 | G -> T | LOC_Os01g15060.1 | downstream_gene_variant ; 1572.0bp to feature; MODIFIER | N | Average:55.996; most accessible tissue: Minghui63 young leaf, score: 70.038 | N | N | N | N |
| vg0108457594 | G -> A | LOC_Os01g15070.1 | missense_variant ; p.Asp57Asn; MODERATE | N | Average:55.996; most accessible tissue: Minghui63 young leaf, score: 70.038 | N | N | N | N |
| vg0108457594 | G -> A | LOC_Os01g15080.1 | upstream_gene_variant ; 365.0bp to feature; MODIFIER | N | Average:55.996; most accessible tissue: Minghui63 young leaf, score: 70.038 | N | N | N | N |
| vg0108457594 | G -> A | LOC_Os01g15090.1 | upstream_gene_variant ; 3478.0bp to feature; MODIFIER | N | Average:55.996; most accessible tissue: Minghui63 young leaf, score: 70.038 | N | N | N | N |
| vg0108457594 | G -> A | LOC_Os01g15060.1 | downstream_gene_variant ; 1572.0bp to feature; MODIFIER | N | Average:55.996; most accessible tissue: Minghui63 young leaf, score: 70.038 | N | N | N | N |