| Variant ID: vg0322193675 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 22193675 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CCGCTTGAGGTTGGGACCTGGGCACGAGCCCTCGTTCAAGCCAAGACACAGAAGGACCGCGGCACAGACCATCCTCGTCTCATACACATAACAAACATAA[C/T]
TGACGTAGAAATTTCCTCTTTATTTGATTACAGATTAAATCAGTCTATACAAGAAGGGGGCCCGAAGGCCTCGGAAGAAGAAGGAGAAGTTATTAAGATT
AATCTTAATAACTTCTCCTTCTTCTTCCGAGGCCTTCGGGCCCCCTTCTTGTATAGACTGATTTAATCTGTAATCAAATAAAGAGGAAATTTCTACGTCA[G/A]
TTATGTTTGTTATGTGTATGAGACGAGGATGGTCTGTGCCGCGGTCCTTCTGTGTCTTGGCTTGAACGAGGGCTCGTGCCCAGGTCCCAACCTCAAGCGG
| 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% | 0.20% | 2.37% | 35.10% | NA |
| All Indica | 2759 | 47.70% | 0.40% | 3.04% | 48.82% | NA |
| All Japonica | 1512 | 93.10% | 0.00% | 0.20% | 6.68% | NA |
| Aus | 269 | 48.70% | 0.00% | 8.92% | 42.38% | NA |
| Indica I | 595 | 25.90% | 0.00% | 5.71% | 68.40% | NA |
| Indica II | 465 | 35.10% | 0.00% | 2.80% | 62.15% | NA |
| Indica III | 913 | 73.20% | 1.00% | 1.31% | 24.53% | NA |
| Indica Intermediate | 786 | 42.20% | 0.30% | 3.18% | 54.33% | NA |
| Temperate Japonica | 767 | 98.60% | 0.00% | 0.13% | 1.30% | NA |
| Tropical Japonica | 504 | 94.80% | 0.00% | 0.40% | 4.76% | NA |
| Japonica Intermediate | 241 | 72.20% | 0.00% | 0.00% | 27.80% | NA |
| VI/Aromatic | 96 | 30.20% | 0.00% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0322193675 | C -> T | LOC_Os03g39920.1 | downstream_gene_variant ; 505.0bp to feature; MODIFIER | silent_mutation | Average:12.585; most accessible tissue: Zhenshan97 panicle, score: 32.308 | N | N | N | N |
| vg0322193675 | C -> T | LOC_Os03g39930.1 | downstream_gene_variant ; 1.0bp to feature; MODIFIER | silent_mutation | Average:12.585; most accessible tissue: Zhenshan97 panicle, score: 32.308 | N | N | N | N |
| vg0322193675 | C -> T | LOC_Os03g39940.1 | downstream_gene_variant ; 4220.0bp to feature; MODIFIER | silent_mutation | Average:12.585; most accessible tissue: Zhenshan97 panicle, score: 32.308 | N | N | N | N |
| vg0322193675 | C -> T | LOC_Os03g39920-LOC_Os03g39930 | intergenic_region ; MODIFIER | silent_mutation | Average:12.585; most accessible tissue: Zhenshan97 panicle, score: 32.308 | N | N | N | N |
| vg0322193675 | C -> DEL | N | N | silent_mutation | Average:12.585; most accessible tissue: Zhenshan97 panicle, score: 32.308 | N | N | N | N |