| Variant ID: vg0317762020 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 17762020 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TGGATGGTGAGGCAGAATTGCCTCCGTTGTTGTAGTCGTTCACGGCACCTCCTCCTGGCGCACCAGCTCCGGATCCGGATCCAGATCCAGCTCCTGTCGG[C/T]
GGCGGCGTACCACCTCCGCCAGCAGTGGCGGCAGCAACTCCAGACATGGCGATGAGCAGTCGTGCGGGAGGCACTCCCCAAAAACCTGATCACCCGCCTA
TAGGCGGGTGATCAGGTTTTTGGGGAGTGCCTCCCGCACGACTGCTCATCGCCATGTCTGGAGTTGCTGCCGCCACTGCTGGCGGAGGTGGTACGCCGCC[G/A]
CCGACAGGAGCTGGATCTGGATCCGGATCCGGAGCTGGTGCGCCAGGAGGAGGTGCCGTGAACGACTACAACAACGGAGGCAATTCTGCCTCACCATCCA
| 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 | 52.40% | 0.30% | 5.18% | 42.19% | NA |
| All Indica | 2759 | 34.80% | 0.40% | 7.21% | 57.56% | NA |
| All Japonica | 1512 | 86.40% | 0.00% | 0.93% | 12.70% | NA |
| Aus | 269 | 24.20% | 0.00% | 10.04% | 65.80% | NA |
| Indica I | 595 | 17.60% | 0.00% | 3.03% | 79.33% | NA |
| Indica II | 465 | 26.00% | 0.60% | 7.74% | 65.59% | NA |
| Indica III | 913 | 53.10% | 0.50% | 9.20% | 37.13% | NA |
| Indica Intermediate | 786 | 31.70% | 0.50% | 7.76% | 60.05% | NA |
| Temperate Japonica | 767 | 99.90% | 0.00% | 0.00% | 0.13% | NA |
| Tropical Japonica | 504 | 66.50% | 0.00% | 2.78% | 30.75% | NA |
| Japonica Intermediate | 241 | 85.10% | 0.00% | 0.00% | 14.94% | NA |
| VI/Aromatic | 96 | 90.60% | 0.00% | 2.08% | 7.29% | NA |
| Intermediate | 90 | 63.30% | 0.00% | 3.33% | 33.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0317762020 | C -> T | LOC_Os03g31190.1 | synonymous_variant ; p.Pro16Pro; LOW | synonymous_codon | Average:5.609; most accessible tissue: Minghui63 flag leaf, score: 9.254 | N | N | N | N |
| vg0317762020 | C -> DEL | LOC_Os03g31190.1 | N | frameshift_variant | Average:5.609; most accessible tissue: Minghui63 flag leaf, score: 9.254 | N | N | N | N |