| Variant ID: vg0322195244 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 22195244 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
ACCGTGCTGTTCGCGGCGGCCAAGGCCTGTAGGAAGGGCTCCACGCTCAGTGGGGCAGCGGAAGACGTGCCGGACTCGGGGGCGTCCCTCGAAGCTGGCT[C/T]
GTCCCAAGTGTCGCCCGAGGGGTCGGGCCCGAGCGGCACGCCCGCGGCCTCGTCGTGGGTGGCCTCGGAAGTTGTCGTCCCCTCGGGCGGAGTCGGGTCG
CGACCCGACTCCGCCCGAGGGGACGACAACTTCCGAGGCCACCCACGACGAGGCCGCGGGCGTGCCGCTCGGGCCCGACCCCTCGGGCGACACTTGGGAC[G/A]
AGCCAGCTTCGAGGGACGCCCCCGAGTCCGGCACGTCTTCCGCTGCCCCACTGAGCGTGGAGCCCTTCCTACAGGCCTTGGCCGCCGCGAACAGCACGGT
| 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 | 12.80% | 0.30% | 21.56% | 65.38% | NA |
| All Indica | 2759 | 0.80% | 0.00% | 23.20% | 76.04% | NA |
| All Japonica | 1512 | 37.60% | 0.80% | 16.53% | 45.04% | NA |
| Aus | 269 | 0.00% | 0.00% | 36.80% | 63.20% | NA |
| Indica I | 595 | 0.50% | 0.00% | 16.64% | 82.86% | NA |
| Indica II | 465 | 1.30% | 0.00% | 4.73% | 93.98% | NA |
| Indica III | 913 | 0.30% | 0.00% | 42.06% | 57.61% | NA |
| Indica Intermediate | 786 | 1.10% | 0.00% | 17.18% | 81.68% | NA |
| Temperate Japonica | 767 | 25.40% | 0.10% | 21.77% | 52.67% | NA |
| Tropical Japonica | 504 | 59.10% | 1.60% | 9.92% | 29.37% | NA |
| Japonica Intermediate | 241 | 31.50% | 1.20% | 13.69% | 53.53% | NA |
| VI/Aromatic | 96 | 1.00% | 0.00% | 18.75% | 80.21% | NA |
| Intermediate | 90 | 15.60% | 0.00% | 13.33% | 71.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0322195244 | C -> T | LOC_Os03g39930.1 | 5_prime_UTR_variant ; 123.0bp to feature; MODIFIER | silent_mutation | Average:16.319; most accessible tissue: Minghui63 panicle, score: 29.741 | N | N | N | N |
| vg0322195244 | C -> T | LOC_Os03g39920.1 | downstream_gene_variant ; 2074.0bp to feature; MODIFIER | silent_mutation | Average:16.319; most accessible tissue: Minghui63 panicle, score: 29.741 | N | N | N | N |
| vg0322195244 | C -> T | LOC_Os03g39940.1 | downstream_gene_variant ; 2651.0bp to feature; MODIFIER | silent_mutation | Average:16.319; most accessible tissue: Minghui63 panicle, score: 29.741 | N | N | N | N |
| vg0322195244 | C -> DEL | N | N | silent_mutation | Average:16.319; most accessible tissue: Minghui63 panicle, score: 29.741 | N | N | N | N |