| Variant ID: vg0317762015 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 17762015 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TCCGCTGGATGGTGAGGCAGAATTGCCTCCGTTGTTGTAGTCGTTCACGGCACCTCCTCCTGGCGCACCAGCTCCGGATCCGGATCCAGATCCAGCTCCT[G/A]
TCGGCGGCGGCGTACCACCTCCGCCAGCAGTGGCGGCAGCAACTCCAGACATGGCGATGAGCAGTCGTGCGGGAGGCACTCCCCAAAAACCTGATCACCC
GGGTGATCAGGTTTTTGGGGAGTGCCTCCCGCACGACTGCTCATCGCCATGTCTGGAGTTGCTGCCGCCACTGCTGGCGGAGGTGGTACGCCGCCGCCGA[C/T]
AGGAGCTGGATCTGGATCCGGATCCGGAGCTGGTGCGCCAGGAGGAGGTGCCGTGAACGACTACAACAACGGAGGCAATTCTGCCTCACCATCCAGCGGA
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 40.40% | 4.50% | 15.95% | 39.12% | NA |
| All Indica | 2759 | 15.70% | 7.60% | 24.57% | 52.05% | NA |
| All Japonica | 1512 | 86.00% | 0.00% | 1.39% | 12.63% | NA |
| Aus | 269 | 17.80% | 0.00% | 13.75% | 68.40% | NA |
| Indica I | 595 | 11.30% | 0.20% | 15.29% | 73.28% | NA |
| Indica II | 465 | 12.30% | 5.40% | 23.01% | 59.35% | NA |
| Indica III | 913 | 21.00% | 14.50% | 28.59% | 35.93% | NA |
| Indica Intermediate | 786 | 15.00% | 6.70% | 27.86% | 50.38% | NA |
| Temperate Japonica | 767 | 99.90% | 0.00% | 0.00% | 0.13% | NA |
| Tropical Japonica | 504 | 65.70% | 0.00% | 3.97% | 30.36% | NA |
| Japonica Intermediate | 241 | 84.20% | 0.00% | 0.41% | 15.35% | NA |
| VI/Aromatic | 96 | 85.40% | 0.00% | 6.25% | 8.33% | NA |
| Intermediate | 90 | 52.20% | 1.10% | 13.33% | 33.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0317762015 | G -> A | LOC_Os03g31190.1 | missense_variant ; p.Thr18Ile; MODERATE | nonsynonymous_codon ; T18I | Average:5.609; most accessible tissue: Minghui63 flag leaf, score: 9.254 | unknown | unknown | DELETERIOUS | 0.01 |
| vg0317762015 | G -> DEL | LOC_Os03g31190.1 | N | frameshift_variant | Average:5.609; most accessible tissue: Minghui63 flag leaf, score: 9.254 | N | N | N | N |