| Variant ID: vg0322195295 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 22195295 |
| Reference Allele: C | Alternative Allele: T,G |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GGGGCAGCGGAAGACGTGCCGGACTCGGGGGCGTCCCTCGAAGCTGGCTCGTCCCAAGTGTCGCCCGAGGGGTCGGGCCCGAGCGGCACGCCCGCGGCCT[C/T,G]
GTCGTGGGTGGCCTCGGAAGTTGTCGTCCCCTCGGGCGGAGTCGGGTCGGGGGTTTGGCAGGCCGCCTGGCGTGCGCGCGCCGCCTCTGCCTCCCGGACG
CGTCCGGGAGGCAGAGGCGGCGCGCGCACGCCAGGCGGCCTGCCAAACCCCCGACCCGACTCCGCCCGAGGGGACGACAACTTCCGAGGCCACCCACGAC[G/A,C]
AGGCCGCGGGCGTGCCGCTCGGGCCCGACCCCTCGGGCGACACTTGGGACGAGCCAGCTTCGAGGGACGCCCCCGAGTCCGGCACGTCTTCCGCTGCCCC
| 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 | 8.80% | 1.90% | 17.75% | 71.54% | G: 0.06% |
| All Indica | 2759 | 0.50% | 0.10% | 23.96% | 75.46% | NA |
| All Japonica | 1512 | 25.90% | 5.40% | 4.30% | 64.22% | G: 0.20% |
| Aus | 269 | 0.00% | 0.00% | 34.20% | 65.80% | NA |
| Indica I | 595 | 0.20% | 0.00% | 14.79% | 85.04% | NA |
| Indica II | 465 | 0.90% | 0.00% | 5.59% | 93.55% | NA |
| Indica III | 913 | 0.40% | 0.00% | 44.03% | 55.53% | NA |
| Indica Intermediate | 786 | 0.50% | 0.40% | 18.45% | 80.66% | NA |
| Temperate Japonica | 767 | 16.60% | 0.00% | 5.61% | 77.84% | NA |
| Tropical Japonica | 504 | 38.50% | 15.90% | 2.38% | 42.66% | G: 0.60% |
| Japonica Intermediate | 241 | 29.00% | 0.80% | 4.15% | 65.98% | NA |
| VI/Aromatic | 96 | 1.00% | 0.00% | 14.58% | 84.38% | NA |
| Intermediate | 90 | 11.10% | 3.30% | 7.78% | 77.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0322195295 | C -> T | LOC_Os03g39930.1 | 5_prime_UTR_variant ; 174.0bp to feature; MODIFIER | silent_mutation | Average:19.019; most accessible tissue: Minghui63 panicle, score: 38.588 | N | N | N | N |
| vg0322195295 | C -> T | LOC_Os03g39920.1 | downstream_gene_variant ; 2125.0bp to feature; MODIFIER | silent_mutation | Average:19.019; most accessible tissue: Minghui63 panicle, score: 38.588 | N | N | N | N |
| vg0322195295 | C -> T | LOC_Os03g39940.1 | downstream_gene_variant ; 2600.0bp to feature; MODIFIER | silent_mutation | Average:19.019; most accessible tissue: Minghui63 panicle, score: 38.588 | N | N | N | N |
| vg0322195295 | C -> DEL | N | N | silent_mutation | Average:19.019; most accessible tissue: Minghui63 panicle, score: 38.588 | N | N | N | N |
| vg0322195295 | C -> G | LOC_Os03g39930.1 | 5_prime_UTR_variant ; 174.0bp to feature; MODIFIER | silent_mutation | Average:19.019; most accessible tissue: Minghui63 panicle, score: 38.588 | N | N | N | N |
| vg0322195295 | C -> G | LOC_Os03g39920.1 | downstream_gene_variant ; 2125.0bp to feature; MODIFIER | silent_mutation | Average:19.019; most accessible tissue: Minghui63 panicle, score: 38.588 | N | N | N | N |
| vg0322195295 | C -> G | LOC_Os03g39940.1 | downstream_gene_variant ; 2600.0bp to feature; MODIFIER | silent_mutation | Average:19.019; most accessible tissue: Minghui63 panicle, score: 38.588 | N | N | N | N |