| Variant ID: vg0136520805 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 36520805 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
AAACCTTCAAAGCCTGCAGATAATTAGTTTTTCATTTCATAAATAGACAATACTACATGGACCAGTGTATTTAAAATTTCAACATATACTTCTATTTTTT[A/T]
AAAAAAACAGCATACACTCATATATGTATGGAAAGATGAAGTACAAAATACTGCGTAGCAAATTCTACCTATGTGTACCCTCTTAATTAAAAAAAAATCA
TGATTTTTTTTTAATTAAGAGGGTACACATAGGTAGAATTTGCTACGCAGTATTTTGTACTTCATCTTTCCATACATATATGAGTGTATGCTGTTTTTTT[T/A]
AAAAAATAGAAGTATATGTTGAAATTTTAAATACACTGGTCCATGTAGTATTGTCTATTTATGAAATGAAAAACTAATTATCTGCAGGCTTTGAAGGTTT
| 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 | 48.60% | 0.10% | 16.46% | 34.79% | NA |
| All Indica | 2759 | 19.20% | 0.00% | 23.92% | 56.80% | NA |
| All Japonica | 1512 | 97.60% | 0.20% | 0.60% | 1.65% | NA |
| Aus | 269 | 49.40% | 0.00% | 36.43% | 14.13% | NA |
| Indica I | 595 | 10.80% | 0.00% | 19.83% | 69.41% | NA |
| Indica II | 465 | 30.10% | 0.00% | 26.67% | 43.23% | NA |
| Indica III | 913 | 15.20% | 0.00% | 23.66% | 61.12% | NA |
| Indica Intermediate | 786 | 23.90% | 0.10% | 25.70% | 50.25% | NA |
| Temperate Japonica | 767 | 99.00% | 0.00% | 0.13% | 0.91% | NA |
| Tropical Japonica | 504 | 97.40% | 0.40% | 0.79% | 1.39% | NA |
| Japonica Intermediate | 241 | 93.40% | 0.40% | 1.66% | 4.56% | NA |
| VI/Aromatic | 96 | 93.80% | 1.00% | 5.21% | 0.00% | NA |
| Intermediate | 90 | 77.80% | 0.00% | 6.67% | 15.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0136520805 | A -> T | LOC_Os01g63030.1 | downstream_gene_variant ; 4192.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0136520805 | A -> T | LOC_Os01g63040.1 | intron_variant ; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0136520805 | A -> DEL | N | N | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |