| Variant ID: vg0204738973 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr02 | Position: 4738973 |
| Reference Allele: AAG | Alternative Allele: A,GAG |
| Primary Allele: AAG | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CCGGCCACCGCTCGCCGGCCATCGCCTGTCGTCGTCCTCCTCCATGGTGCGTCACCGATCTGTGGGCTGGGATGATGGATCGATGCATATCCCAAAAAAA[AAG/A,GAG]
AGGAAAAAATAAAGTGGGGGCGAGAGTGGTTGGTTGGGTACGGGAAAAATAGAATATATACTGGAATCTGGGAAGTTGTTTTTATCGAAGTAAATCATTT
AAATGATTTACTTCGATAAAAACAACTTCCCAGATTCCAGTATATATTCTATTTTTCCCGTACCCAACCAACCACTCTCGCCCCCACTTTATTTTTTCCT[CTT/T,CTC]
TTTTTTTGGGATATGCATCGATCCATCATCCCAGCCCACAGATCGGTGACGCACCATGGAGGAGGACGACGACAGGCGATGGCCGGCGAGCGGTGGCCGG
| Populations | Population Size | Frequency of AAG(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 38.90% | 14.80% | 4.21% | 41.01% | GAG: 1.04% |
| All Indica | 2759 | 22.90% | 12.50% | 5.18% | 59.44% | NA |
| All Japonica | 1512 | 55.50% | 21.00% | 3.31% | 17.06% | GAG: 3.11% |
| Aus | 269 | 85.50% | 7.40% | 0.37% | 6.69% | NA |
| Indica I | 595 | 0.80% | 18.30% | 10.08% | 70.76% | NA |
| Indica II | 465 | 31.20% | 13.50% | 4.73% | 50.54% | NA |
| Indica III | 913 | 32.60% | 8.40% | 3.94% | 54.98% | NA |
| Indica Intermediate | 786 | 23.40% | 12.10% | 3.18% | 61.32% | NA |
| Temperate Japonica | 767 | 88.30% | 2.00% | 2.48% | 4.04% | GAG: 3.26% |
| Tropical Japonica | 504 | 16.10% | 45.80% | 3.77% | 34.33% | NA |
| Japonica Intermediate | 241 | 33.60% | 29.90% | 4.98% | 22.41% | GAG: 9.13% |
| VI/Aromatic | 96 | 91.70% | 6.20% | 1.04% | 1.04% | NA |
| Intermediate | 90 | 55.60% | 14.40% | 4.44% | 23.33% | GAG: 2.22% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0204738973 | AAG -> A | LOC_Os02g09220.1 | upstream_gene_variant ; 1070.0bp to feature; MODIFIER | silent_mutation | Average:41.596; most accessible tissue: Callus, score: 57.213 | N | N | N | N |
| vg0204738973 | AAG -> A | LOC_Os02g09210-LOC_Os02g09220 | intergenic_region ; MODIFIER | silent_mutation | Average:41.596; most accessible tissue: Callus, score: 57.213 | N | N | N | N |
| vg0204738973 | AAG -> GAG | LOC_Os02g09220.1 | upstream_gene_variant ; 1071.0bp to feature; MODIFIER | silent_mutation | Average:41.596; most accessible tissue: Callus, score: 57.213 | N | N | N | N |
| vg0204738973 | AAG -> GAG | LOC_Os02g09210-LOC_Os02g09220 | intergenic_region ; MODIFIER | silent_mutation | Average:41.596; most accessible tissue: Callus, score: 57.213 | N | N | N | N |
| vg0204738973 | AAG -> DEL | N | N | silent_mutation | Average:41.596; most accessible tissue: Callus, score: 57.213 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0204738973 | 1.10E-06 | 7.72E-07 | mr1550 | 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 |
| vg0204738973 | 3.09E-06 | NA | mr1757 | 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 |
| vg0204738973 | NA | 7.99E-06 | mr1549_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 |