| Variant ID: vg0415575320 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 15575320 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
ATTGCTAAATTATTTTATACCAAATGCTTACAAGAGACAGCAAAAACAGTTTAAATCTATATTTCTAATCACTGGTGGAGAAACCAATCTTTGGTCGGTC[G/A]
GCCGAAATCCACAATAGTCCCGATTCCACTAAAAACCGGGACTAAAGATGATCTTTAGTCCTGGTTGGTGGCTACAGTGGGCATATTTGATCTTTAGTCC
GGACTAAAGATCAAATATGCCCACTGTAGCCACCAACCAGGACTAAAGATCATCTTTAGTCCCGGTTTTTAGTGGAATCGGGACTATTGTGGATTTCGGC[C/T]
GACCGACCAAAGATTGGTTTCTCCACCAGTGATTAGAAATATAGATTTAAACTGTTTTTGCTGTCTCTTGTAAGCATTTGGTATAAAATAATTTAGCAAT
| 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 | 71.00% | 6.60% | 0.55% | 21.86% | NA |
| All Indica | 2759 | 72.50% | 11.20% | 0.58% | 15.80% | NA |
| All Japonica | 1512 | 78.50% | 0.00% | 0.46% | 21.03% | NA |
| Aus | 269 | 4.80% | 0.00% | 0.00% | 95.17% | NA |
| Indica I | 595 | 89.60% | 0.30% | 1.01% | 9.08% | NA |
| Indica II | 465 | 68.80% | 4.30% | 0.43% | 26.45% | NA |
| Indica III | 913 | 59.80% | 24.40% | 0.66% | 15.12% | NA |
| Indica Intermediate | 786 | 76.30% | 8.00% | 0.25% | 15.39% | NA |
| Temperate Japonica | 767 | 60.20% | 0.00% | 0.65% | 39.11% | NA |
| Tropical Japonica | 504 | 98.80% | 0.00% | 0.20% | 0.99% | NA |
| Japonica Intermediate | 241 | 94.20% | 0.00% | 0.41% | 5.39% | NA |
| VI/Aromatic | 96 | 90.60% | 0.00% | 1.04% | 8.33% | NA |
| Intermediate | 90 | 76.70% | 4.40% | 2.22% | 16.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0415575320 | G -> DEL | N | N | silent_mutation | Average:11.603; most accessible tissue: Zhenshan97 flower, score: 18.233 | N | N | N | N |
| vg0415575320 | G -> A | LOC_Os04g26680.1 | downstream_gene_variant ; 4994.0bp to feature; MODIFIER | silent_mutation | Average:11.603; most accessible tissue: Zhenshan97 flower, score: 18.233 | N | N | N | N |
| vg0415575320 | G -> A | LOC_Os04g26690.1 | intron_variant ; MODIFIER | silent_mutation | Average:11.603; most accessible tissue: Zhenshan97 flower, score: 18.233 | N | N | N | N |