| Variant ID: vg1107679454 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 7679454 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GTGGCCAGAATGCGGATACTGATGCGGTGATTTTAGAAGGAAAAGAACTGAGTTATATGTGAACAGATGAAAGGCTTACCTGAATTGTCGGAGCTGGAAG[G/A]
AATGTCAGTCATCGACTCTGTCCTTGAATCTGACGAAGTCTCTGAAAGATGGTGTTGAAATATGTCATTAGTGTGATTGGCTATAGATTTGTACATATAG
CTATATGTACAAATCTATAGCCAATCACACTAATGACATATTTCAACACCATCTTTCAGAGACTTCGTCAGATTCAAGGACAGAGTCGATGACTGACATT[C/T]
CTTCCAGCTCCGACAATTCAGGTAAGCCTTTCATCTGTTCACATATAACTCAGTTCTTTTCCTTCTAAAATCACCGCATCAGTATCCGCATTCTGGCCAC
| 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 | 39.40% | 1.40% | 7.36% | 51.88% | NA |
| All Indica | 2759 | 6.20% | 0.00% | 9.42% | 84.34% | NA |
| All Japonica | 1512 | 86.70% | 4.20% | 4.70% | 4.43% | NA |
| Aus | 269 | 88.50% | 0.00% | 3.35% | 8.18% | NA |
| Indica I | 595 | 4.50% | 0.00% | 7.73% | 87.73% | NA |
| Indica II | 465 | 2.80% | 0.00% | 7.31% | 89.89% | NA |
| Indica III | 913 | 3.20% | 0.00% | 12.05% | 84.78% | NA |
| Indica Intermediate | 786 | 13.00% | 0.10% | 8.91% | 77.99% | NA |
| Temperate Japonica | 767 | 85.30% | 7.70% | 4.43% | 2.61% | NA |
| Tropical Japonica | 504 | 91.90% | 0.20% | 4.56% | 3.37% | NA |
| Japonica Intermediate | 241 | 80.50% | 1.20% | 5.81% | 12.45% | NA |
| VI/Aromatic | 96 | 97.90% | 0.00% | 0.00% | 2.08% | NA |
| Intermediate | 90 | 53.30% | 0.00% | 8.89% | 37.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1107679454 | G -> A | LOC_Os11g13900.1 | missense_variant ; p.Pro112Ser; MODERATE | nonsynonymous_codon ; P112S | Average:4.94; most accessible tissue: Minghui63 panicle, score: 7.125 | unknown | unknown | TOLERATED | 0.34 |
| vg1107679454 | G -> DEL | LOC_Os11g13900.1 | N | frameshift_variant | Average:4.94; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |