| Variant ID: vg0322193716 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 22193716 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CAAGACACAGAAGGACCGCGGCACAGACCATCCTCGTCTCATACACATAACAAACATAACTGACGTAGAAATTTCCTCTTTATTTGATTACAGATTAAAT[C/T]
AGTCTATACAAGAAGGGGGCCCGAAGGCCTCGGAAGAAGAAGGAGAAGTTATTAAGATTGGCGGGGGCCTGGGGGCTCACTCCGGCGCCCCCGGGCCGTC
GACGGCCCGGGGGCGCCGGAGTGAGCCCCCAGGCCCCCGCCAATCTTAATAACTTCTCCTTCTTCTTCCGAGGCCTTCGGGCCCCCTTCTTGTATAGACT[G/A]
ATTTAATCTGTAATCAAATAAAGAGGAAATTTCTACGTCAGTTATGTTTGTTATGTGTATGAGACGAGGATGGTCTGTGCCGCGGTCCTTCTGTGTCTTG
| 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 | 62.30% | 0.10% | 1.35% | 36.16% | NA |
| All Indica | 2759 | 48.20% | 0.10% | 1.12% | 50.60% | NA |
| All Japonica | 1512 | 92.70% | 0.30% | 0.33% | 6.75% | NA |
| Aus | 269 | 48.70% | 0.00% | 8.92% | 42.38% | NA |
| Indica I | 595 | 25.50% | 0.00% | 0.67% | 73.78% | NA |
| Indica II | 465 | 35.10% | 0.00% | 2.15% | 62.80% | NA |
| Indica III | 913 | 74.60% | 0.10% | 0.99% | 24.32% | NA |
| Indica Intermediate | 786 | 42.50% | 0.10% | 1.02% | 56.36% | NA |
| Temperate Japonica | 767 | 98.60% | 0.00% | 0.00% | 1.43% | NA |
| Tropical Japonica | 504 | 94.20% | 0.40% | 0.60% | 4.76% | NA |
| Japonica Intermediate | 241 | 70.50% | 0.80% | 0.83% | 27.80% | NA |
| VI/Aromatic | 96 | 26.00% | 1.00% | 3.12% | 69.79% | NA |
| Intermediate | 90 | 65.60% | 0.00% | 1.11% | 33.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0322193716 | C -> T | LOC_Os03g39930.1 | 3_prime_UTR_variant ; 77.0bp to feature; MODIFIER | silent_mutation | Average:12.265; most accessible tissue: Zhenshan97 panicle, score: 32.308 | N | N | N | N |
| vg0322193716 | C -> T | LOC_Os03g39920.1 | downstream_gene_variant ; 546.0bp to feature; MODIFIER | silent_mutation | Average:12.265; most accessible tissue: Zhenshan97 panicle, score: 32.308 | N | N | N | N |
| vg0322193716 | C -> T | LOC_Os03g39940.1 | downstream_gene_variant ; 4179.0bp to feature; MODIFIER | silent_mutation | Average:12.265; most accessible tissue: Zhenshan97 panicle, score: 32.308 | N | N | N | N |
| vg0322193716 | C -> DEL | N | N | silent_mutation | Average:12.265; most accessible tissue: Zhenshan97 panicle, score: 32.308 | N | N | N | N |