| Variant ID: vg1105160158 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 5160158 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CGTGTGCAGGGATGCATGGTATGGTGTTGCAGACTTGACAGAACCGCTGAATGTATGAGCGAAGTGACTCATCATCCCTTCGCTGGACTGCATGTAAGTC[C/T]
GCTTCTTCACCTGGGCGCGGATATGTGCCTTGAAAGTTCATGGTGAACTGTTGGCACAAATCCTCCCAAGAGTGGACGGACGCGGGTGGCAAGTTCATTA
TAATGAACTTGCCACCCGCGTCCGTCCACTCTTGGGAGGATTTGTGCCAACAGTTCACCATGAACTTTCAAGGCACATATCCGCGCCCAGGTGAAGAAGC[G/A]
GACTTACATGCAGTCCAGCGAAGGGATGATGAGTCACTTCGCTCATACATTCAGCGGTTCTGTCAAGTCTGCAACACCATACCATGCATCCCTGCACACG
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 40.30% | 0.10% | 24.08% | 35.57% | NA |
| All Indica | 2759 | 16.70% | 0.00% | 33.85% | 49.40% | NA |
| All Japonica | 1512 | 86.70% | 0.10% | 5.09% | 8.07% | NA |
| Aus | 269 | 12.30% | 0.00% | 35.32% | 52.42% | NA |
| Indica I | 595 | 13.40% | 0.00% | 17.31% | 69.24% | NA |
| Indica II | 465 | 7.50% | 0.00% | 28.39% | 64.09% | NA |
| Indica III | 913 | 16.80% | 0.00% | 55.09% | 28.15% | NA |
| Indica Intermediate | 786 | 24.70% | 0.00% | 24.94% | 50.38% | NA |
| Temperate Japonica | 767 | 90.10% | 0.00% | 2.35% | 7.56% | NA |
| Tropical Japonica | 504 | 83.90% | 0.40% | 6.75% | 8.93% | NA |
| Japonica Intermediate | 241 | 81.70% | 0.00% | 10.37% | 7.88% | NA |
| VI/Aromatic | 96 | 58.30% | 1.00% | 18.75% | 21.88% | NA |
| Intermediate | 90 | 46.70% | 0.00% | 15.56% | 37.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1105160158 | C -> T | LOC_Os11g09660.1 | synonymous_variant ; p.Ala321Ala; LOW | synonymous_codon | Average:5.954; most accessible tissue: Zhenshan97 flower, score: 11.396 | N | N | N | N |
| vg1105160158 | C -> DEL | LOC_Os11g09660.1 | N | frameshift_variant | Average:5.954; most accessible tissue: Zhenshan97 flower, score: 11.396 | N | N | N | N |