| Variant ID: vg1221992283 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 21992283 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
AGGGAACTAACTTGTGCGGCTATTACGTGTGCGAGTATTGCCACTGCCTTGCAGACCAAATCATCACCACAAGAGAGCTCGATGTAAGTACAAATAAATT[C/T]
AAAATTTCATTACGTAGCGATTTCTTGTTTAATTACTAATCAATTTCATACATTCATATAGTTTATTCGCATGAGGGATAACCTGACCACACACAAGGAA
TTCCTTGTGTGTGGTCAGGTTATCCCTCATGCGAATAAACTATATGAATGTATGAAATTGATTAGTAATTAAACAAGAAATCGCTACGTAATGAAATTTT[G/A]
AATTTATTTGTACTTACATCGAGCTCTCTTGTGGTGATGATTTGGTCTGCAAGGCAGTGGCAATACTCGCACACGTAATAGCCGCACAAGTTAGTTCCCT
| 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 | 65.00% | 0.10% | 3.72% | 31.19% | NA |
| All Indica | 2759 | 52.10% | 0.20% | 4.10% | 43.57% | NA |
| All Japonica | 1512 | 91.10% | 0.00% | 0.13% | 8.73% | NA |
| Aus | 269 | 43.90% | 0.00% | 8.92% | 47.21% | NA |
| Indica I | 595 | 64.20% | 0.80% | 3.87% | 31.09% | NA |
| Indica II | 465 | 69.50% | 0.20% | 2.58% | 27.74% | NA |
| Indica III | 913 | 32.70% | 0.00% | 5.81% | 61.45% | NA |
| Indica Intermediate | 786 | 55.20% | 0.00% | 3.18% | 41.60% | NA |
| Temperate Japonica | 767 | 96.50% | 0.00% | 0.00% | 3.52% | NA |
| Tropical Japonica | 504 | 79.80% | 0.00% | 0.40% | 19.84% | NA |
| Japonica Intermediate | 241 | 97.90% | 0.00% | 0.00% | 2.07% | NA |
| VI/Aromatic | 96 | 63.50% | 0.00% | 35.42% | 1.04% | NA |
| Intermediate | 90 | 83.30% | 0.00% | 3.33% | 13.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1221992283 | C -> DEL | N | N | silent_mutation | Average:6.928; most accessible tissue: Minghui63 flower, score: 12.456 | N | N | N | N |
| vg1221992283 | C -> T | LOC_Os12g35980.1 | upstream_gene_variant ; 2797.0bp to feature; MODIFIER | silent_mutation | Average:6.928; most accessible tissue: Minghui63 flower, score: 12.456 | N | N | N | N |
| vg1221992283 | C -> T | LOC_Os12g35970.1 | intron_variant ; MODIFIER | silent_mutation | Average:6.928; most accessible tissue: Minghui63 flower, score: 12.456 | N | N | N | N |