| Variant ID: vg0103668583 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr01 | Position: 3668583 |
| Reference Allele: G | Alternative Allele: GA |
| Primary Allele: G | Secondary Allele: GA |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 295. )
CTGGTACTGTTAATAATGAGATATTACGAGGAACAAGGTATTTGGTGTACCAGAAATCAACATTAGAAGATATTTGTCTTTCAATACCTCCAAGGATGGG[G/GA]
AAAAAATTCAAAAGTAATTTAAGGAAAAAATTTCTCTGTTTCCAAAGAAAAAGTGAGTAAGCATATAGAGAACACAAAAAACATACCCAATCAAGCACTC
GAGTGCTTGATTGGGTATGTTTTTTGTGTTCTCTATATGCTTACTCACTTTTTCTTTGGAAACAGAGAAATTTTTTCCTTAAATTACTTTTGAATTTTTT[C/TC]
CCCATCCTTGGAGGTATTGAAAGACAAATATCTTCTAATGTTGATTTCTGGTACACCAAATACCTTGTTCCTCGTAATATCTCATTATTAACAGTACCAG
| Populations | Population Size | Frequency of G(primary allele) | Frequency of GA(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 79.10% | 20.70% | 0.30% | 0.00% | NA |
| All Indica | 2759 | 77.70% | 21.80% | 0.43% | 0.00% | NA |
| All Japonica | 1512 | 79.40% | 20.50% | 0.13% | 0.00% | NA |
| Aus | 269 | 92.20% | 7.80% | 0.00% | 0.00% | NA |
| Indica I | 595 | 47.70% | 51.60% | 0.67% | 0.00% | NA |
| Indica II | 465 | 97.00% | 2.80% | 0.22% | 0.00% | NA |
| Indica III | 913 | 81.70% | 18.30% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 84.50% | 14.60% | 0.89% | 0.00% | NA |
| Temperate Japonica | 767 | 98.30% | 1.70% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 47.80% | 52.00% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 85.10% | 14.50% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 64.60% | 35.40% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 90.00% | 10.00% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0103668583 | G -> GA | LOC_Os01g07620.1 | upstream_gene_variant ; 2538.0bp to feature; MODIFIER | silent_mutation | Average:47.186; most accessible tissue: Minghui63 flower, score: 68.171 | N | N | N | N |
| vg0103668583 | G -> GA | LOC_Os01g07610.1 | downstream_gene_variant ; 4265.0bp to feature; MODIFIER | silent_mutation | Average:47.186; most accessible tissue: Minghui63 flower, score: 68.171 | N | N | N | N |
| vg0103668583 | G -> GA | LOC_Os01g07630.1 | intron_variant ; MODIFIER | silent_mutation | Average:47.186; most accessible tissue: Minghui63 flower, score: 68.171 | N | N | N | N |