| Variant ID: vg0211510634 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr02 | Position: 11510634 |
| Reference Allele: GGA | Alternative Allele: G,AGA |
| Primary Allele: AGA | Secondary Allele: GGA |
Inferred Ancestral Allele: Not determined.
AAAACAGTGGAAGACTAGGGCGACGACCACAGGCACTTGACGGCAGGCACAAGCTAGACACCAAAGCCTTCATCTTCCAGGAACTCCTCTTCTGGGTTGG[GGA/G,AGA]
AAAATTGAGCAAGATTGAGTACAACCACAGTACTCAGCAAGACACACCCACGGATGCAGAATAAATGCAAAGGAGTACAAGGGAGTTATAATAAAAGGGG
CCCCTTTTATTATAACTCCCTTGTACTCCTTTGCATTTATTCTGCATCCGTGGGTGTGTCTTGCTGAGTACTGTGGTTGTACTCAATCTTGCTCAATTTT[TCC/C,TCT]
CCAACCCAGAAGAGGAGTTCCTGGAAGATGAAGGCTTTGGTGTCTAGCTTGTGCCTGCCGTCAAGTGCCTGTGGTCGTCGCCCTAGTCTTCCACTGTTTT
| Populations | Population Size | Frequency of AGA(primary allele) | Frequency of GGA(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 62.00% | 34.70% | 0.72% | 2.54% | NA |
| All Indica | 2759 | 95.40% | 0.90% | 0.58% | 3.08% | NA |
| All Japonica | 1512 | 1.80% | 98.10% | 0.07% | 0.00% | NA |
| Aus | 269 | 81.00% | 0.40% | 5.58% | 13.01% | NA |
| Indica I | 595 | 99.80% | 0.00% | 0.00% | 0.17% | NA |
| Indica II | 465 | 97.40% | 1.90% | 0.22% | 0.43% | NA |
| Indica III | 913 | 91.10% | 0.50% | 0.77% | 7.56% | NA |
| Indica Intermediate | 786 | 95.80% | 1.50% | 1.02% | 1.65% | NA |
| Temperate Japonica | 767 | 1.00% | 98.80% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 2.80% | 97.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 2.10% | 97.90% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 8.30% | 91.70% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 50.00% | 47.80% | 2.22% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0211510634 | GGA -> G | LOC_Os02g19670.1 | intron_variant ; MODIFIER | N | Average:44.924; most accessible tissue: Zhenshan97 panicle, score: 61.671 | N | N | N | N |
| vg0211510634 | GGA -> AGA | LOC_Os02g19670.1 | intron_variant ; MODIFIER | silent_mutation | Average:44.924; most accessible tissue: Zhenshan97 panicle, score: 61.671 | N | N | N | N |
| vg0211510634 | GGA -> DEL | N | N | silent_mutation | Average:44.924; most accessible tissue: Zhenshan97 panicle, score: 61.671 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0211510634 | 2.25E-07 | 9.46E-08 | mr1004 | 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 |
| vg0211510634 | 1.01E-06 | 3.26E-12 | mr1005 | 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 |
| vg0211510634 | 6.03E-07 | NA | mr1011 | 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 |
| vg0211510634 | NA | 2.66E-10 | mr1683 | 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 |