| Variant ID: vg1000477812 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 477812 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TTGTGAGAAAATAAGGATTCATGATAATCAAAATATTCTTACCATGAAATCGTTGTCGAGAATATTTGAACAAACAAAGAACCTTCGACCCAATATCGTA[G/A]
GCTTTATGGAACGAAGAACCTGACAATGGATCCTTCGTGTGAACAAACGGAACCATAGCTAAAGGCCACCCGCATTGCAATGCATTTTCCACATACCATC
GATGGTATGTGGAAAATGCATTGCAATGCGGGTGGCCTTTAGCTATGGTTCCGTTTGTTCACACGAAGGATCCATTGTCAGGTTCTTCGTTCCATAAAGC[C/T]
TACGATATTGGGTCGAAGGTTCTTTGTTTGTTCAAATATTCTCGACAACGATTTCATGGTAAGAATATTTTGATTATCATGAATCCTTATTTTCTCACAA
| 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 | 89.80% | 2.70% | 1.14% | 6.37% | NA |
| All Indica | 2759 | 95.90% | 0.40% | 0.62% | 3.04% | NA |
| All Japonica | 1512 | 98.10% | 1.30% | 0.00% | 0.53% | NA |
| Aus | 269 | 8.20% | 19.00% | 13.75% | 59.11% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.10% | 0.00% | 0.22% | 0.65% | NA |
| Indica III | 913 | 94.00% | 0.30% | 0.66% | 5.04% | NA |
| Indica Intermediate | 786 | 93.30% | 1.00% | 1.27% | 4.45% | NA |
| Temperate Japonica | 767 | 99.90% | 0.00% | 0.00% | 0.13% | NA |
| Tropical Japonica | 504 | 99.40% | 0.60% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 90.00% | 7.10% | 0.00% | 2.90% | NA |
| VI/Aromatic | 96 | 15.60% | 41.70% | 0.00% | 42.71% | NA |
| Intermediate | 90 | 83.30% | 6.70% | 0.00% | 10.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1000477812 | G -> A | LOC_Os10g01740.1 | 5_prime_UTR_variant ; 56.0bp to feature; MODIFIER | silent_mutation | Average:24.471; most accessible tissue: Callus, score: 37.292 | N | N | N | N |
| vg1000477812 | G -> A | LOC_Os10g01730.1 | downstream_gene_variant ; 1758.0bp to feature; MODIFIER | silent_mutation | Average:24.471; most accessible tissue: Callus, score: 37.292 | N | N | N | N |
| vg1000477812 | G -> A | LOC_Os10g01750.1 | downstream_gene_variant ; 4872.0bp to feature; MODIFIER | silent_mutation | Average:24.471; most accessible tissue: Callus, score: 37.292 | N | N | N | N |
| vg1000477812 | G -> DEL | N | N | silent_mutation | Average:24.471; most accessible tissue: Callus, score: 37.292 | N | N | N | N |