| Variant ID: vg0317762042 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 17762042 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TCCGTTGTTGTAGTCGTTCACGGCACCTCCTCCTGGCGCACCAGCTCCGGATCCGGATCCAGATCCAGCTCCTGTCGGCGGCGGCGTACCACCTCCGCCA[G/A]
CAGTGGCGGCAGCAACTCCAGACATGGCGATGAGCAGTCGTGCGGGAGGCACTCCCCAAAAACCTGATCACCCGCCTACCCGGTGCAGATCTCAGGCGAA
TTCGCCTGAGATCTGCACCGGGTAGGCGGGTGATCAGGTTTTTGGGGAGTGCCTCCCGCACGACTGCTCATCGCCATGTCTGGAGTTGCTGCCGCCACTG[C/T]
TGGCGGAGGTGGTACGCCGCCGCCGACAGGAGCTGGATCTGGATCCGGATCCGGAGCTGGTGCGCCAGGAGGAGGTGCCGTGAACGACTACAACAACGGA
| 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 | 36.60% | 1.00% | 8.74% | 53.72% | NA |
| All Indica | 2759 | 9.60% | 1.40% | 12.76% | 76.19% | NA |
| All Japonica | 1512 | 85.30% | 0.30% | 0.99% | 13.49% | NA |
| Aus | 269 | 17.50% | 0.70% | 11.52% | 70.26% | NA |
| Indica I | 595 | 6.20% | 0.70% | 8.91% | 84.20% | NA |
| Indica II | 465 | 4.90% | 1.30% | 6.67% | 87.10% | NA |
| Indica III | 913 | 14.80% | 2.20% | 18.62% | 64.40% | NA |
| Indica Intermediate | 786 | 8.90% | 1.30% | 12.47% | 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% | 0.83% | 15.35% | NA |
| VI/Aromatic | 96 | 87.50% | 0.00% | 4.17% | 8.33% | NA |
| Intermediate | 90 | 47.80% | 0.00% | 12.22% | 40.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0317762042 | G -> A | LOC_Os03g31190.1 | missense_variant ; p.Ala9Val; MODERATE | nonsynonymous_codon ; A9V | Average:5.609; most accessible tissue: Minghui63 flag leaf, score: 9.254 | unknown | unknown | DELETERIOUS | 0.03 |
| vg0317762042 | G -> DEL | LOC_Os03g31190.1 | N | frameshift_variant | Average:5.609; most accessible tissue: Minghui63 flag leaf, score: 9.254 | N | N | N | N |