| Variant ID: vg1221991935 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 21991935 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
GGAGGCCTGCACCGTCAACGTATATGACTCAATGGATAAAAAAGAGTCTACATTTGACAAGGTTTTCGAACTTATAGACAGGTACCGTCATAAGTTCCTT[T/C]
GTTAATTAAGAAAATCTTGTTATGTTAATTGCTACTATGAATTATAGCTTTAAACTCCATGTAGGGCTTGGTATCGGTTCCGTCATTTGGTCCGCGGCAA
TTGCCGCGGACCAAATGACGGAACCGATACCAAGCCCTACATGGAGTTTAAAGCTATAATTCATAGTAGCAATTAACATAACAAGATTTTCTTAATTAAC[A/G]
AAGGAACTTATGACGGTACCTGTCTATAAGTTCGAAAACCTTGTCAAATGTAGACTCTTTTTTATCCATTGAGTCATATACGTTGACGGTGCAGGCCTCC
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 58.50% | 0.10% | 6.39% | 35.00% | NA |
| All Indica | 2759 | 45.00% | 0.00% | 5.87% | 49.15% | NA |
| All Japonica | 1512 | 85.20% | 0.30% | 4.63% | 9.85% | NA |
| Aus | 269 | 40.90% | 0.00% | 10.41% | 48.70% | NA |
| Indica I | 595 | 53.60% | 0.00% | 6.39% | 40.00% | NA |
| Indica II | 465 | 60.60% | 0.00% | 3.87% | 35.48% | NA |
| Indica III | 913 | 28.60% | 0.00% | 6.57% | 64.84% | NA |
| Indica Intermediate | 786 | 48.20% | 0.00% | 5.85% | 45.93% | NA |
| Temperate Japonica | 767 | 88.30% | 0.30% | 6.00% | 5.48% | NA |
| Tropical Japonica | 504 | 78.20% | 0.00% | 1.59% | 20.24% | NA |
| Japonica Intermediate | 241 | 90.00% | 1.20% | 6.64% | 2.07% | NA |
| VI/Aromatic | 96 | 60.40% | 0.00% | 37.50% | 2.08% | NA |
| Intermediate | 90 | 75.60% | 0.00% | 6.67% | 17.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1221991935 | T -> C | LOC_Os12g35980.1 | upstream_gene_variant ; 3145.0bp to feature; MODIFIER | silent_mutation | Average:10.404; most accessible tissue: Minghui63 flower, score: 21.533 | N | N | N | N |
| vg1221991935 | T -> C | LOC_Os12g35970.1 | intron_variant ; MODIFIER | silent_mutation | Average:10.404; most accessible tissue: Minghui63 flower, score: 21.533 | N | N | N | N |
| vg1221991935 | T -> DEL | N | N | silent_mutation | Average:10.404; most accessible tissue: Minghui63 flower, score: 21.533 | N | N | N | N |