| Variant ID: vg0322195519 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 22195519 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GGCCTCCTCCCGAGCGGCCTTCTCAGCCTGGCGAACCCGGACGGCCTCCTGGGCAGCCTCCTCGGCTTCCCGGAGGCGGTCCGCGGCTTCTCGCCGGTCA[G/A]
CTTCCCGCCTCCGGGCCTCCGCTGTCGCCGTCTCCTCGGCCTCAGACCGGCCGGACTTGGAATGGCGGGGGGGGGGCGCGACGGGATCTCGCTGAGGCAG
CTGCCTCAGCGAGATCCCGTCGCGCCCCCCCCCCGCCATTCCAAGTCCGGCCGGTCTGAGGCCGAGGAGACGGCGACAGCGGAGGCCCGGAGGCGGGAAG[C/T]
TGACCGGCGAGAAGCCGCGGACCGCCTCCGGGAAGCCGAGGAGGCTGCCCAGGAGGCCGTCCGGGTTCGCCAGGCTGAGAAGGCCGCTCGGGAGGAGGCC
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 11.30% | 0.30% | 19.45% | 69.02% | NA |
| All Indica | 2759 | 1.00% | 0.00% | 25.01% | 74.01% | NA |
| All Japonica | 1512 | 32.40% | 0.80% | 7.28% | 59.52% | NA |
| Aus | 269 | 0.40% | 0.00% | 33.83% | 65.80% | NA |
| Indica I | 595 | 0.30% | 0.00% | 15.46% | 84.20% | NA |
| Indica II | 465 | 1.10% | 0.00% | 5.38% | 93.55% | NA |
| Indica III | 913 | 1.40% | 0.00% | 45.89% | 52.68% | NA |
| Indica Intermediate | 786 | 0.90% | 0.00% | 19.59% | 79.52% | NA |
| Temperate Japonica | 767 | 19.70% | 0.00% | 5.35% | 74.97% | NA |
| Tropical Japonica | 504 | 53.80% | 1.80% | 9.72% | 34.72% | NA |
| Japonica Intermediate | 241 | 28.20% | 1.20% | 8.30% | 62.24% | NA |
| VI/Aromatic | 96 | 2.10% | 0.00% | 16.67% | 81.25% | NA |
| Intermediate | 90 | 14.40% | 0.00% | 13.33% | 72.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0322195519 | G -> A | LOC_Os03g39930.1 | 5_prime_UTR_premature_start_codon_gain_variant ; LOW | silent_mutation | Average:23.952; most accessible tissue: Minghui63 panicle, score: 42.799 | N | N | N | N |
| vg0322195519 | G -> A | LOC_Os03g39930.1 | 5_prime_UTR_variant ; 398.0bp to feature; MODIFIER | silent_mutation | Average:23.952; most accessible tissue: Minghui63 panicle, score: 42.799 | N | N | N | N |
| vg0322195519 | G -> A | LOC_Os03g39920.1 | downstream_gene_variant ; 2349.0bp to feature; MODIFIER | silent_mutation | Average:23.952; most accessible tissue: Minghui63 panicle, score: 42.799 | N | N | N | N |
| vg0322195519 | G -> A | LOC_Os03g39940.1 | downstream_gene_variant ; 2376.0bp to feature; MODIFIER | silent_mutation | Average:23.952; most accessible tissue: Minghui63 panicle, score: 42.799 | N | N | N | N |
| vg0322195519 | G -> DEL | N | N | silent_mutation | Average:23.952; most accessible tissue: Minghui63 panicle, score: 42.799 | N | N | N | N |