| Variant ID: vg0915238376 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr09 | Position: 15238376 |
| Reference Allele: G | Alternative Allele: A,GAAAGTAACGGTACACGTTTTGAAAAAAAA |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
ATGGTGGTGAATAAGCTGTGTTCTTTTTTATGGGTTCTCAACCCATCTCTATCGTGCACGTTTTTTTCAAACTGTTAAACGGTACACGTTTTGAAAAAAA[G/A,GAAAGTAACGGTACACGTTTTGAAAAAAAA]
TTTATATATGAAAGTTGCTTTAAAAAATCATATTAATTATTTTTTAAAGTTTTTTTATAGCTAGCACTTAATTAATCACGTGTTAATCTATCGTTCCATT
AATGGAACGATAGATTAACACGTGATTAATTAAGTGCTAGCTATAAAAAAACTTTAAAAAATAATTAATATGATTTTTTAAAGCAACTTTCATATATAAA[C/T,TTTTTTTTCAAAACGTGTACCGTTACTTTC]
TTTTTTTCAAAACGTGTACCGTTTAACAGTTTGAAAAAAACGTGCACGATAGAGATGGGTTGAGAACCCATAAAAAAGAACACAGCTTATTCACCACCAT
| 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 | 95.90% | 3.30% | 0.74% | 0.00% | GAAAGTAACGGTACACGTTTTGAAAAAAAA: 0.11% |
| All Indica | 2759 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 87.80% | 9.80% | 2.18% | 0.00% | GAAAGTAACGGTACACGTTTTGAAAAAAAA: 0.26% |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 99.00% | 0.90% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 71.80% | 23.20% | 4.96% | 0.00% | NA |
| Japonica Intermediate | 241 | 85.50% | 10.00% | 2.90% | 0.00% | GAAAGTAACGGTACACGTTTTGAAAAAAAA: 1.66% |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 91.10% | 5.60% | 2.22% | 0.00% | GAAAGTAACGGTACACGTTTTGAAAAAAAA: 1.11% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0915238376 | G -> GAAAGTAACGGTACACGTTTTGAAAAAAAA | LOC_Os09g25420.1 | upstream_gene_variant ; 553.0bp to feature; MODIFIER | silent_mutation | Average:69.325; most accessible tissue: Zhenshan97 flower, score: 82.481 | N | N | N | N |
| vg0915238376 | G -> GAAAGTAACGGTACACGTTTTGAAAAAAAA | LOC_Os09g25410.1 | downstream_gene_variant ; 2373.0bp to feature; MODIFIER | silent_mutation | Average:69.325; most accessible tissue: Zhenshan97 flower, score: 82.481 | N | N | N | N |
| vg0915238376 | G -> GAAAGTAACGGTACACGTTTTGAAAAAAAA | LOC_Os09g25430.1 | downstream_gene_variant ; 2069.0bp to feature; MODIFIER | silent_mutation | Average:69.325; most accessible tissue: Zhenshan97 flower, score: 82.481 | N | N | N | N |
| vg0915238376 | G -> GAAAGTAACGGTACACGTTTTGAAAAAAAA | LOC_Os09g25410.2 | downstream_gene_variant ; 2373.0bp to feature; MODIFIER | silent_mutation | Average:69.325; most accessible tissue: Zhenshan97 flower, score: 82.481 | N | N | N | N |
| vg0915238376 | G -> GAAAGTAACGGTACACGTTTTGAAAAAAAA | LOC_Os09g25420-LOC_Os09g25430 | intergenic_region ; MODIFIER | silent_mutation | Average:69.325; most accessible tissue: Zhenshan97 flower, score: 82.481 | N | N | N | N |
| vg0915238376 | G -> A | LOC_Os09g25420.1 | upstream_gene_variant ; 552.0bp to feature; MODIFIER | silent_mutation | Average:69.325; most accessible tissue: Zhenshan97 flower, score: 82.481 | N | N | N | N |
| vg0915238376 | G -> A | LOC_Os09g25410.1 | downstream_gene_variant ; 2372.0bp to feature; MODIFIER | silent_mutation | Average:69.325; most accessible tissue: Zhenshan97 flower, score: 82.481 | N | N | N | N |
| vg0915238376 | G -> A | LOC_Os09g25430.1 | downstream_gene_variant ; 2070.0bp to feature; MODIFIER | silent_mutation | Average:69.325; most accessible tissue: Zhenshan97 flower, score: 82.481 | N | N | N | N |
| vg0915238376 | G -> A | LOC_Os09g25410.2 | downstream_gene_variant ; 2372.0bp to feature; MODIFIER | silent_mutation | Average:69.325; most accessible tissue: Zhenshan97 flower, score: 82.481 | N | N | N | N |
| vg0915238376 | G -> A | LOC_Os09g25420-LOC_Os09g25430 | intergenic_region ; MODIFIER | silent_mutation | Average:69.325; most accessible tissue: Zhenshan97 flower, score: 82.481 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0915238376 | NA | 6.20E-07 | mr1205 | 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 |
| vg0915238376 | NA | 6.25E-08 | mr1206 | 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 |
| vg0915238376 | NA | 1.93E-06 | mr1596 | 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 |
| vg0915238376 | 4.82E-06 | 4.82E-06 | mr1663 | 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 |
| vg0915238376 | NA | 1.29E-08 | mr1668 | Jap_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 |
| vg0915238376 | NA | 5.70E-06 | mr1668_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 |