| Variant ID: vg0611845202 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 11845202 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CCGCGGTTAAGTCTATAAATGATAGCCGATCGGCCAGATGCCGATGACATATCGATCGGCAATCATGAATAAGTAAAGAAAAACTAAACCTACTTGATCG[G/A]
CTGTAGATATTAACATATATAATCCTTATATTGATGTTTATTTAAATCGAGTGATTGGGATAGATCGGTTATCATACCGAGACAGTATAAATCACTCAGA
TCTGAGTGATTTATACTGTCTCGGTATGATAACCGATCTATCCCAATCACTCGATTTAAATAAACATCAATATAAGGATTATATATGTTAATATCTACAG[C/T]
CGATCAAGTAGGTTTAGTTTTTCTTTACTTATTCATGATTGCCGATCGATATGTCATCGGCATCTGGCCGATCGGCTATCATTTATAGACTTAACCGCGG
| 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 | 61.40% | 0.60% | 9.69% | 28.33% | NA |
| All Indica | 2759 | 41.10% | 1.10% | 14.93% | 42.95% | NA |
| All Japonica | 1512 | 93.80% | 0.00% | 0.86% | 5.29% | NA |
| Aus | 269 | 76.20% | 0.00% | 2.23% | 21.56% | NA |
| Indica I | 595 | 34.80% | 0.70% | 14.12% | 50.42% | NA |
| Indica II | 465 | 56.30% | 0.60% | 11.18% | 31.83% | NA |
| Indica III | 913 | 36.40% | 1.10% | 17.42% | 45.13% | NA |
| Indica Intermediate | 786 | 42.20% | 1.50% | 14.89% | 41.35% | NA |
| Temperate Japonica | 767 | 98.30% | 0.00% | 0.52% | 1.17% | NA |
| Tropical Japonica | 504 | 87.30% | 0.00% | 1.19% | 11.51% | NA |
| Japonica Intermediate | 241 | 93.40% | 0.00% | 1.24% | 5.39% | NA |
| VI/Aromatic | 96 | 78.10% | 0.00% | 19.79% | 2.08% | NA |
| Intermediate | 90 | 75.60% | 0.00% | 8.89% | 15.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0611845202 | G -> A | LOC_Os06g20570.1 | upstream_gene_variant ; 899.0bp to feature; MODIFIER | silent_mutation | Average:12.895; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |
| vg0611845202 | G -> A | LOC_Os06g20580.1 | upstream_gene_variant ; 1510.0bp to feature; MODIFIER | silent_mutation | Average:12.895; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |
| vg0611845202 | G -> A | LOC_Os06g20570-LOC_Os06g20580 | intergenic_region ; MODIFIER | silent_mutation | Average:12.895; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |
| vg0611845202 | G -> DEL | N | N | silent_mutation | Average:12.895; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |