| Variant ID: vg0317762025 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 17762025 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GGTGAGGCAGAATTGCCTCCGTTGTTGTAGTCGTTCACGGCACCTCCTCCTGGCGCACCAGCTCCGGATCCGGATCCAGATCCAGCTCCTGTCGGCGGCG[G/T]
CGTACCACCTCCGCCAGCAGTGGCGGCAGCAACTCCAGACATGGCGATGAGCAGTCGTGCGGGAGGCACTCCCCAAAAACCTGATCACCCGCCTACCCGG
CCGGGTAGGCGGGTGATCAGGTTTTTGGGGAGTGCCTCCCGCACGACTGCTCATCGCCATGTCTGGAGTTGCTGCCGCCACTGCTGGCGGAGGTGGTACG[C/A]
CGCCGCCGACAGGAGCTGGATCTGGATCCGGATCCGGAGCTGGTGCGCCAGGAGGAGGTGCCGTGAACGACTACAACAACGGAGGCAATTCTGCCTCACC
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 51.70% | 0.10% | 4.04% | 44.12% | NA |
| All Indica | 2759 | 33.70% | 0.20% | 5.26% | 60.82% | NA |
| All Japonica | 1512 | 86.30% | 0.00% | 1.06% | 12.63% | NA |
| Aus | 269 | 23.80% | 0.00% | 10.04% | 66.17% | NA |
| Indica I | 595 | 17.80% | 0.00% | 2.69% | 79.50% | NA |
| Indica II | 465 | 26.70% | 0.00% | 3.01% | 70.32% | NA |
| Indica III | 913 | 49.70% | 0.40% | 7.34% | 42.50% | NA |
| Indica Intermediate | 786 | 31.40% | 0.10% | 6.11% | 62.34% | NA |
| Temperate Japonica | 767 | 99.90% | 0.00% | 0.00% | 0.13% | NA |
| Tropical Japonica | 504 | 66.30% | 0.00% | 3.17% | 30.56% | 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 | 64.40% | 0.00% | 1.11% | 34.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0317762025 | G -> T | LOC_Os03g31190.1 | missense_variant ; p.Pro15Thr; MODERATE | nonsynonymous_codon ; P15T | Average:5.609; most accessible tissue: Minghui63 flag leaf, score: 9.254 | unknown | unknown | DELETERIOUS | 0.00 |
| vg0317762025 | G -> DEL | LOC_Os03g31190.1 | N | frameshift_variant | Average:5.609; most accessible tissue: Minghui63 flag leaf, score: 9.254 | N | N | N | N |