| Variant ID: vg1023166693 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr10 | Position: 23166693 |
| Reference Allele: AACTCTGTTATTT | Alternative Allele: A |
| Primary Allele: AACTCTGTTATTT | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CTCCCGTTGGTTCGAAATTTAATTTTAGAAACACTAATTTTCATCAATTTCATCTATTTGCAGCGGAAGATCTATATACAATTCGTATAAACAATAACAA[AACTCTGTTATTT/A]
ACTCTCTGTAAAATTCTCCCGTTGGTTCAAATTTAAACAGAGGTAAAACATGCAAAAACAATTCAAAATTCTATTGTAATTTGCATGAAAATATACAAAA
TTTTGTATATTTTCATGCAAATTACAATAGAATTTTGAATTGTTTTTGCATGTTTTACCTCTGTTTAAATTTGAACCAACGGGAGAATTTTACAGAGAGT[AAATAACAGAGTT/T]
TTGTTATTGTTTATACGAATTGTATATAGATCTTCCGCTGCAAATAGATGAAATTGATGAAAATTAGTGTTTCTAAAATTAAATTTCGAACCAACGGGAG
| Populations | Population Size | Frequency of AACTCTGTTATTT(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 18.50% | 0.20% | 22.15% | 59.12% | NA |
| All Indica | 2759 | 2.20% | 0.00% | 15.88% | 81.91% | NA |
| All Japonica | 1512 | 52.10% | 0.70% | 35.65% | 11.57% | NA |
| Aus | 269 | 0.00% | 0.00% | 1.12% | 98.88% | NA |
| Indica I | 595 | 5.00% | 0.00% | 1.68% | 93.28% | NA |
| Indica II | 465 | 1.50% | 0.00% | 4.30% | 94.19% | NA |
| Indica III | 913 | 0.10% | 0.00% | 33.41% | 66.48% | NA |
| Indica Intermediate | 786 | 2.90% | 0.00% | 13.10% | 83.97% | NA |
| Temperate Japonica | 767 | 70.10% | 0.00% | 25.42% | 4.43% | NA |
| Tropical Japonica | 504 | 31.00% | 1.20% | 51.79% | 16.07% | NA |
| Japonica Intermediate | 241 | 39.00% | 1.70% | 34.44% | 24.90% | NA |
| VI/Aromatic | 96 | 10.40% | 0.00% | 39.58% | 50.00% | NA |
| Intermediate | 90 | 17.80% | 0.00% | 32.22% | 50.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1023166693 | AACTCTGTTATTT -> A | LOC_Os10g42970.1 | upstream_gene_variant ; 4279.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1023166693 | AACTCTGTTATTT -> A | LOC_Os10g42999.1 | upstream_gene_variant ; 2759.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1023166693 | AACTCTGTTATTT -> A | LOC_Os10g42970.2 | upstream_gene_variant ; 4279.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1023166693 | AACTCTGTTATTT -> A | LOC_Os10g42980.1 | intron_variant ; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1023166693 | AACTCTGTTATTT -> DEL | N | N | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |