| Variant ID: vg0317762046 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 17762046 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TTGTTGTAGTCGTTCACGGCACCTCCTCCTGGCGCACCAGCTCCGGATCCGGATCCAGATCCAGCTCCTGTCGGCGGCGGCGTACCACCTCCGCCAGCAG[T/A]
GGCGGCAGCAACTCCAGACATGGCGATGAGCAGTCGTGCGGGAGGCACTCCCCAAAAACCTGATCACCCGCCTACCCGGTGCAGATCTCAGGCGAAGGTG
CACCTTCGCCTGAGATCTGCACCGGGTAGGCGGGTGATCAGGTTTTTGGGGAGTGCCTCCCGCACGACTGCTCATCGCCATGTCTGGAGTTGCTGCCGCC[A/T]
CTGCTGGCGGAGGTGGTACGCCGCCGCCGACAGGAGCTGGATCTGGATCCGGATCCGGAGCTGGTGCGCCAGGAGGAGGTGCCGTGAACGACTACAACAA
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 36.60% | 0.90% | 8.91% | 53.60% | NA |
| All Indica | 2759 | 9.70% | 1.30% | 12.94% | 76.01% | NA |
| All Japonica | 1512 | 85.30% | 0.30% | 1.06% | 13.43% | NA |
| Aus | 269 | 17.10% | 0.70% | 11.52% | 70.63% | NA |
| Indica I | 595 | 6.20% | 0.70% | 8.40% | 84.71% | NA |
| Indica II | 465 | 5.40% | 1.30% | 7.10% | 86.24% | NA |
| Indica III | 913 | 15.30% | 1.90% | 18.84% | 63.96% | NA |
| Indica Intermediate | 786 | 8.50% | 1.10% | 12.98% | 77.35% | NA |
| Temperate Japonica | 767 | 99.70% | 0.00% | 0.13% | 0.13% | NA |
| Tropical Japonica | 504 | 63.90% | 0.80% | 2.38% | 32.94% | NA |
| Japonica Intermediate | 241 | 83.80% | 0.00% | 1.24% | 14.94% | NA |
| VI/Aromatic | 96 | 86.50% | 0.00% | 5.21% | 8.33% | NA |
| Intermediate | 90 | 47.80% | 0.00% | 13.33% | 38.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0317762046 | T -> A | LOC_Os03g31190.1 | missense_variant ; p.Thr8Ser; MODERATE | nonsynonymous_codon ; T8S | Average:5.609; most accessible tissue: Minghui63 flag leaf, score: 9.254 | unknown | unknown | DELETERIOUS | 0.04 |
| vg0317762046 | T -> DEL | LOC_Os03g31190.1 | N | frameshift_variant | Average:5.609; most accessible tissue: Minghui63 flag leaf, score: 9.254 | N | N | N | N |