| Variant ID: vg0807399977 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 7399977 |
| Reference Allele: G | Alternative Allele: C |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
TCGCATTTATCCTAATACATCTTTTTGTATCTTGCAGAAAAGACGTGTTGTCGGAGTCGTCCGTCAAGCCTGAGTGGAAGAGCTAGCCCTAGAAGGAATT[G/C]
GAGCAGGCAAGTGACGTAATAATATAAATGATTGTTATATTTGTAATGCAATTAATTAAGATTATTAGACCTGTAATTGGACTTATCATATAAGATTGTG
CACAATCTTATATGATAAGTCCAATTACAGGTCTAATAATCTTAATTAATTGCATTACAAATATAACAATCATTTATATTATTACGTCACTTGCCTGCTC[C/G]
AATTCCTTCTAGGGCTAGCTCTTCCACTCAGGCTTGACGGACGACTCCGACAACACGTCTTTTCTGCAAGATACAAAAAGATGTATTAGGATAAATGCGA
| Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 33.10% | 0.50% | 3.70% | 62.74% | NA |
| All Indica | 2759 | 14.40% | 0.00% | 2.72% | 82.89% | NA |
| All Japonica | 1512 | 73.70% | 1.50% | 6.15% | 18.65% | NA |
| Aus | 269 | 3.00% | 0.00% | 1.49% | 95.54% | NA |
| Indica I | 595 | 33.10% | 0.00% | 3.53% | 63.36% | NA |
| Indica II | 465 | 15.50% | 0.00% | 1.94% | 82.58% | NA |
| Indica III | 913 | 2.30% | 0.00% | 1.20% | 96.50% | NA |
| Indica Intermediate | 786 | 13.60% | 0.00% | 4.33% | 82.06% | NA |
| Temperate Japonica | 767 | 56.10% | 2.90% | 8.87% | 32.20% | NA |
| Tropical Japonica | 504 | 94.20% | 0.00% | 2.98% | 2.78% | NA |
| Japonica Intermediate | 241 | 87.10% | 0.00% | 4.15% | 8.71% | NA |
| VI/Aromatic | 96 | 4.20% | 0.00% | 2.08% | 93.75% | NA |
| Intermediate | 90 | 43.30% | 1.10% | 1.11% | 54.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0807399977 | G -> C | LOC_Os08g12500.1 | intron_variant ; MODIFIER | silent_mutation | Average:5.412; most accessible tissue: Minghui63 flower, score: 9.27 | N | N | N | N |
| vg0807399977 | G -> DEL | N | N | silent_mutation | Average:5.412; most accessible tissue: Minghui63 flower, score: 9.27 | N | N | N | N |