| Variant ID: vg1021203353 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 21203353 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TATTAGCCAATTTGAACAAATCCCAAAACTCTACAGATTTACAGAACAAACAATACCATCATCTCTGCAGTTCATGCTTTTCTTGCGTTGCTACACAAGC[T/A]
GATTTTATTGATCAAGTTGTGTTCAGTATTCTTATGTATGCAAAAATATGTAGGTTATTTTTTAAAAAAATGTTATAATTTATTAATGCTGTTCTTAGCA
TGCTAAGAACAGCATTAATAAATTATAACATTTTTTTAAAAAATAACCTACATATTTTTGCATACATAAGAATACTGAACACAACTTGATCAATAAAATC[A/T]
GCTTGTGTAGCAACGCAAGAAAAGCATGAACTGCAGAGATGATGGTATTGTTTGTTCTGTAAATCTGTAGAGTTTTGGGATTTGTTCAAATTGGCTAATA
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 65.10% | 34.70% | 0.21% | 0.00% | NA |
| All Indica | 2759 | 98.60% | 1.10% | 0.29% | 0.00% | NA |
| All Japonica | 1512 | 1.70% | 98.30% | 0.07% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 98.00% | 1.70% | 0.34% | 0.00% | NA |
| Indica II | 465 | 98.50% | 1.30% | 0.22% | 0.00% | NA |
| Indica III | 913 | 99.60% | 0.30% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 98.10% | 1.40% | 0.51% | 0.00% | NA |
| Temperate Japonica | 767 | 1.80% | 98.00% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 1.40% | 98.60% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 1.70% | 98.30% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 11.50% | 88.50% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 56.70% | 42.20% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1021203353 | T -> A | LOC_Os10g39680.1 | upstream_gene_variant ; 2347.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1021203353 | T -> A | LOC_Os10g39670.1 | intron_variant ; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |