| Variant ID: vg0909672381 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 9672381 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
AACAGTTCCTTTAGGGAAGATTGAACAATATACAAAGCATAATCTTAGCTCATGGGGCATATTATAATATATTATCTTGAATGATGGAAATAGTGGTGAA[A/G]
TTTTGTCTTGGGGATAATCTTCCTCTATCTTCCACATTTCTTCATCCTTTGCAGCTTGCCAAATCTCACGCCTTTGTCGTTGAGCATTCACCACAGAACC
GGTTCTGTGGTGAATGCTCAACGACAAAGGCGTGAGATTTGGCAAGCTGCAAAGGATGAAGAAATGTGGAAGATAGAGGAAGATTATCCCCAAGACAAAA[T/C]
TTCACCACTATTTCCATCATTCAAGATAATATATTATAATATGCCCCATGAGCTAAGATTATGCTTTGTATATTGTTCAATCTTCCCTAAAGGAACTGTT
| 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 | 92.40% | 7.40% | 0.11% | 0.00% | NA |
| All Indica | 2759 | 98.60% | 1.40% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 79.60% | 20.20% | 0.26% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 94.30% | 5.50% | 0.17% | 0.00% | NA |
| Indica II | 465 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 82.00% | 17.50% | 0.52% | 0.00% | NA |
| Tropical Japonica | 504 | 76.20% | 23.80% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 78.80% | 21.20% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 91.10% | 8.90% | 0.00% | 0.00% | NA |
Rice quantitative trait nucleotides (QTNs) and inferred QTN effects are from Wei et al., Nature Genetics, 2021.
| Category | Variant ID | Chrom | Pos | Gene | MSU | RAP | Alt_Allele_Function | Ref_geno | Alt_geno |
|---|---|---|---|---|---|---|---|---|---|
| Biotic Stress | vg0909672381 | Chr9 | 9672381 | Pii/HIT7/pi5-1 | LOC_Os09g15840 | Os09g0327600 | increasing blast resistance | A | G |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0909672381 | A -> G | LOC_Os09g15840.1 | downstream_gene_variant ; 1619.0bp to feature; MODIFIER | silent_mutation | Average:52.664; most accessible tissue: Zhenshan97 root, score: 66.289 | N | N | N | N |
| vg0909672381 | A -> G | LOC_Os09g15835-LOC_Os09g15840 | intergenic_region ; MODIFIER | silent_mutation | Average:52.664; most accessible tissue: Zhenshan97 root, score: 66.289 | N | N | N | N |