| Variant ID: vg0710347343 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 10347343 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
GAGCGAACGAACGTGAACGAGCTAGGGAACGTGAACGAGCGAACGAACGAGGACGAACGTTAACGTGAAATGCAATATATATATATATATATATATATAT[A/G]
TATATGTTACTTCGCATTTATCCTAATACATTTTTTTGTATCTTGCAGAAAAGACGTGTTGTCGGAGTCGTCCGTCAAGCCTGAGTGGAAGAGCTAGCCC
GGGCTAGCTCTTCCACTCAGGCTTGACGGACGACTCCGACAACACGTCTTTTCTGCAAGATACAAAAAAATGTATTAGGATAAATGCGAAGTAACATATA[T/C]
ATATATATATATATATATATATATATTGCATTTCACGTTAACGTTCGTCCTCGTTCGTTCGCTCGTTCACGTTCCCTAGCTCGTTCACGTTCGTTCGCTC
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 5.50% | 0.40% | 23.36% | 70.78% | NA |
| All Indica | 2759 | 0.80% | 0.50% | 6.52% | 92.21% | NA |
| All Japonica | 1512 | 14.80% | 0.00% | 51.72% | 33.47% | NA |
| Aus | 269 | 3.70% | 1.10% | 37.17% | 57.99% | NA |
| Indica I | 595 | 0.20% | 0.50% | 4.71% | 94.62% | NA |
| Indica II | 465 | 1.30% | 0.00% | 5.59% | 93.12% | NA |
| Indica III | 913 | 1.00% | 0.80% | 3.83% | 94.41% | NA |
| Indica Intermediate | 786 | 0.60% | 0.50% | 11.58% | 87.28% | NA |
| Temperate Japonica | 767 | 6.90% | 0.00% | 47.85% | 45.24% | NA |
| Tropical Japonica | 504 | 30.00% | 0.00% | 49.60% | 20.44% | NA |
| Japonica Intermediate | 241 | 8.30% | 0.00% | 68.46% | 23.24% | NA |
| VI/Aromatic | 96 | 3.10% | 1.00% | 16.67% | 79.17% | NA |
| Intermediate | 90 | 1.10% | 0.00% | 28.89% | 70.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0710347343 | A -> DEL | N | N | silent_mutation | Average:6.509; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |
| vg0710347343 | A -> G | LOC_Os07g17500.1 | downstream_gene_variant ; 1913.0bp to feature; MODIFIER | silent_mutation | Average:6.509; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |
| vg0710347343 | A -> G | LOC_Os07g17510.1 | intron_variant ; MODIFIER | silent_mutation | Average:6.509; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |