| Variant ID: vg0919120424 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr09 | Position: 19120424 |
| Reference Allele: GA | Alternative Allele: G |
| Primary Allele: GA | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
AGCCTTCACCTCGCTTGCAACTTTAGCTAGGGAGACAGCAACTGAAGAGAACACAAAGATATGTTCAAGCTTCAGGGATTTTGTATTTTGGACCGTTAAA[GA/G]
AAAAAATATTATAAAGCAAGTGAGTACGAATCTATATATGACTACAATGAACAATCAGCAACAGAGAATTCAATTCAGCACATATAGCAAGCAGGACATT
AATGTCCTGCTTGCTATATGTGCTGAATTGAATTCTCTGTTGCTGATTGTTCATTGTAGTCATATATAGATTCGTACTCACTTGCTTTATAATATTTTTT[TC/C]
TTTAACGGTCCAAAATACAAAATCCCTGAAGCTTGAACATATCTTTGTGTTCTCTTCAGTTGCTGTCTCCCTAGCTAAAGTTGCAAGCGAGGTGAAGGCT
| Populations | Population Size | Frequency of GA(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 98.00% | 2.00% | 0.04% | 0.00% | NA |
| All Indica | 2759 | 97.30% | 2.60% | 0.07% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 92.20% | 7.80% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Indica II | 465 | 95.90% | 3.90% | 0.22% | 0.00% | NA |
| Indica III | 913 | 98.10% | 1.90% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 95.30% | 4.60% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 100.00% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0919120424 | GA -> G | LOC_Os09g32020.1 | upstream_gene_variant ; 2408.0bp to feature; MODIFIER | silent_mutation | Average:64.61; most accessible tissue: Minghui63 flower, score: 75.455 | N | N | N | N |
| vg0919120424 | GA -> G | LOC_Os09g32025.1 | upstream_gene_variant ; 1286.0bp to feature; MODIFIER | silent_mutation | Average:64.61; most accessible tissue: Minghui63 flower, score: 75.455 | N | N | N | N |
| vg0919120424 | GA -> G | LOC_Os09g32040.1 | downstream_gene_variant ; 1401.0bp to feature; MODIFIER | silent_mutation | Average:64.61; most accessible tissue: Minghui63 flower, score: 75.455 | N | N | N | N |
| vg0919120424 | GA -> G | LOC_Os09g32050.1 | downstream_gene_variant ; 4965.0bp to feature; MODIFIER | silent_mutation | Average:64.61; most accessible tissue: Minghui63 flower, score: 75.455 | N | N | N | N |
| vg0919120424 | GA -> G | LOC_Os09g32050.2 | downstream_gene_variant ; 4976.0bp to feature; MODIFIER | silent_mutation | Average:64.61; most accessible tissue: Minghui63 flower, score: 75.455 | N | N | N | N |
| vg0919120424 | GA -> G | LOC_Os09g32030.1 | intron_variant ; MODIFIER | silent_mutation | Average:64.61; most accessible tissue: Minghui63 flower, score: 75.455 | N | N | N | N |