| Variant ID: vg0404393271 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr04 | Position: 4393271 |
| Reference Allele: TAG | Alternative Allele: CAG,T |
| Primary Allele: CAG | Secondary Allele: TAG |
Inferred Ancestral Allele: Not determined.
CAGTTGAGTCGGGTTCCGACTCCATGTGCAGAGGATCCTCATGGATAATCTCGACCTCCGGGATGGCTTCGCTTCGGCCGAAAGAATCATTCTCTAAGAT[TAG/CAG,T]
ATCTAAGAGTTCTCTTCCTTCGGCGGTTGTCTTGTGTGCGAAGGATCCTCCGGCGGAGATATCAAGATTTACGGTAGACTCCTTGTCTAACCCGTACCAA
TTGGTACGGGTTAGACAAGGAGTCTACCGTAAATCTTGATATCTCCGCCGGAGGATCCTTCGCACACAAGACAACCGCCGAAGGAAGAGAACTCTTAGAT[CTA/CTG,A]
ATCTTAGAGAATGATTCTTTCGGCCGAAGCGAAGCCATCCCGGAGGTCGAGATTATCCATGAGGATCCTCTGCACATGGAGTCGGAACCCGACTCAACTG
| Populations | Population Size | Frequency of CAG(primary allele) | Frequency of TAG(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 39.70% | 18.40% | 1.12% | 40.71% | T: 0.04% |
| All Indica | 2759 | 59.20% | 2.50% | 1.16% | 37.08% | NA |
| All Japonica | 1512 | 3.70% | 50.30% | 0.20% | 45.83% | NA |
| Aus | 269 | 34.20% | 7.80% | 5.58% | 51.67% | T: 0.74% |
| Indica I | 595 | 93.90% | 0.50% | 0.17% | 5.38% | NA |
| Indica II | 465 | 64.70% | 4.70% | 1.72% | 28.82% | NA |
| Indica III | 913 | 36.70% | 1.60% | 1.31% | 60.35% | NA |
| Indica Intermediate | 786 | 55.90% | 3.80% | 1.40% | 38.93% | NA |
| Temperate Japonica | 767 | 1.40% | 86.80% | 0.00% | 11.73% | NA |
| Tropical Japonica | 504 | 5.40% | 9.30% | 0.60% | 84.72% | NA |
| Japonica Intermediate | 241 | 7.50% | 19.50% | 0.00% | 73.03% | NA |
| VI/Aromatic | 96 | 52.10% | 1.00% | 1.04% | 45.83% | NA |
| Intermediate | 90 | 50.00% | 20.00% | 2.22% | 27.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0404393271 | TAG -> DEL | N | N | silent_mutation | Average:20.441; most accessible tissue: Zhenshan97 root, score: 44.635 | N | N | N | N |
| vg0404393271 | TAG -> CAG | LOC_Os04g08240.1 | downstream_gene_variant ; 3970.0bp to feature; MODIFIER | silent_mutation | Average:20.441; most accessible tissue: Zhenshan97 root, score: 44.635 | N | N | N | N |
| vg0404393271 | TAG -> CAG | LOC_Os04g08230.1 | intron_variant ; MODIFIER | silent_mutation | Average:20.441; most accessible tissue: Zhenshan97 root, score: 44.635 | N | N | N | N |
| vg0404393271 | TAG -> T | LOC_Os04g08240.1 | downstream_gene_variant ; 3969.0bp to feature; MODIFIER | silent_mutation | Average:20.441; most accessible tissue: Zhenshan97 root, score: 44.635 | N | N | N | N |
| vg0404393271 | TAG -> T | LOC_Os04g08230.1 | intron_variant ; MODIFIER | silent_mutation | Average:20.441; most accessible tissue: Zhenshan97 root, score: 44.635 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0404393271 | 6.71E-06 | NA | mr1235_2 | Ind_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0404393271 | NA | 3.80E-06 | mr1330_2 | Jap_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0404393271 | 3.80E-06 | NA | mr1860_2 | Ind_All | YES | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |