| Variant ID: vg1107679379 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 7679379 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TATCATGATTGTTGATATGCTAATAGTGACTCGGATTTGTTCTCTGTACTGGTAGGCTTGTGTGATAAAATCTCTGTGGCCAGAATGCGGATACTGATGC[G/A]
GTGATTTTAGAAGGAAAAGAACTGAGTTATATGTGAACAGATGAAAGGCTTACCTGAATTGTCGGAGCTGGAAGGAATGTCAGTCATCGACTCTGTCCTT
AAGGACAGAGTCGATGACTGACATTCCTTCCAGCTCCGACAATTCAGGTAAGCCTTTCATCTGTTCACATATAACTCAGTTCTTTTCCTTCTAAAATCAC[C/T]
GCATCAGTATCCGCATTCTGGCCACAGAGATTTTATCACACAAGCCTACCAGTACAGAGAACAAATCCGAGTCACTATTAGCATATCAACAATCATGATA
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 41.80% | 0.20% | 6.77% | 51.21% | NA |
| All Indica | 2759 | 6.80% | 0.10% | 9.82% | 83.29% | NA |
| All Japonica | 1512 | 92.50% | 0.60% | 2.71% | 4.23% | NA |
| Aus | 269 | 91.10% | 0.00% | 0.74% | 8.18% | NA |
| Indica I | 595 | 5.20% | 0.20% | 9.41% | 85.21% | NA |
| Indica II | 465 | 3.40% | 0.00% | 8.82% | 87.74% | NA |
| Indica III | 913 | 3.60% | 0.00% | 11.50% | 84.88% | NA |
| Indica Intermediate | 786 | 13.70% | 0.10% | 8.78% | 77.35% | NA |
| Temperate Japonica | 767 | 95.70% | 1.20% | 0.78% | 2.35% | NA |
| Tropical Japonica | 504 | 92.10% | 0.00% | 4.76% | 3.17% | NA |
| Japonica Intermediate | 241 | 83.00% | 0.00% | 4.56% | 12.45% | NA |
| VI/Aromatic | 96 | 97.90% | 0.00% | 0.00% | 2.08% | NA |
| Intermediate | 90 | 55.60% | 0.00% | 6.67% | 37.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1107679379 | G -> A | LOC_Os11g13910.1 | upstream_gene_variant ; 1027.0bp to feature; MODIFIER | silent_mutation | Average:4.932; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1107679379 | G -> A | LOC_Os11g13920.1 | downstream_gene_variant ; 4001.0bp to feature; MODIFIER | silent_mutation | Average:4.932; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1107679379 | G -> A | LOC_Os11g13900.1 | intron_variant ; MODIFIER | silent_mutation | Average:4.932; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1107679379 | G -> DEL | N | N | silent_mutation | Average:4.932; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |