| Variant ID: vg1208226725 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr12 | Position: 8226725 |
| Reference Allele: A | Alternative Allele: G,ACCGCCCCTTCGCAGCCACCGTCGCCGCTCCTCCGCTGCCATCAGCCCTCTGCAGCTGCCGCCGCCGCCGTTCCTCCGCCGCAACTGCCACCG,ACCGCCCCTTCGCAGCCACCGTCGCCGCTCCTCCGCTGCCGTCGGCCCTCTGCAGCTGCCGCCGCCGCCGTTCCTCCGCCGCAACTGCCACCG,ACCGCCCCTTCGCAGCCACCGTCGCCGCTCCTCCGCTGCCGTTGGCCCTCTGCAGCTACCGCCGCCACCGTTCCTCCGCCGCAACTGCCACCG,ACCGCCCCTTCGTAGCCACCGTCGCCGCTCCTCCGCTGCCGTCGGCCCTCTGCAGCTGCCGCCGCCACCGTTCCTCCGCCGCAACTGCCACCG,ACCGCCCCTTCGCAGCCACCGTCACCGCTCCTCCGCTGCCGTTGGCCCTCTGCAGCTACCGCCGCCACCGTTCCTCCGCCGCAACTGCCACCG |
| Primary Allele: A | Secondary Allele: ACCGCCCCTTCGCAGCCACC GTCGCCGCTCCTCCGCTGCC ATCAGCCCTCTGCAGCTGCC GCCGCCGCCGTTCCTCCGCC GCAACTGCCACCG |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.86, G: 0.13, others allele: 0.00, population size: 72. )
CGCCACCGCCCCTTCGCTCCCAGCGCCGCTGCTCCTCCGCAGCCGTCGGCCCTCCGCAGCTGCCGCCGCCGTCGCTCTTTCCTCCGCCGCAACTGCCGCC[A/G,ACCGCCCCTTCGCAGCCACCGTCGCCGCTCCTCCGCTGCCATCAGCCCTCTGCAGCTGCCGCCGCCGCCGTTCCTCCGCCGCAACTGCCACCG,ACCGCCCCTTCGCAGCCACCGTCGCCGCTCCTCCGCTGCCGTCGGCCCTCTGCAGCTGCCGCCGCCGCCGTTCCTCCGCCGCAACTGCCACCG,ACCGCCCCTTCGCAGCCACCGTCGCCGCTCCTCCGCTGCCGTTGGCCCTCTGCAGCTACCGCCGCCACCGTTCCTCCGCCGCAACTGCCACCG,ACCGCCCCTTCGTAGCCACCGTCGCCGCTCCTCCGCTGCCGTCGGCCCTCTGCAGCTGCCGCCGCCACCGTTCCTCCGCCGCAACTGCCACCG,ACCGCCCCTTCGCAGCCACCGTCACCGCTCCTCCGCTGCCGTTGGCCCTCTGCAGCTACCGCCGCCACCGTTCCTCCGCCGCAACTGCCACCG]
CCGTCGCCGCAGCGCTCGAGGGAGATAGAGAGAGATTAGAGAGAGAGGATAAGAAGCAGGTCAAACAAGCAACTGGGTTAAATAAGTATGGGTAAAATGG
CCATTTTACCCATACTTATTTAACCCAGTTGCTTGTTTGACCTGCTTCTTATCCTCTCTCTCTAATCTCTCTCTATCTCCCTCGAGCGCTGCGGCGACGG[T/C,CGGTGGCAGTTGCGGCGGAGGAACGGCGGCGGCGGCAGCTGCAGAGGGCTGATGGCAGCGGAGGAGCGGCGACGGTGGCTGCGAAGGGGCGGT,CGGTGGCAGTTGCGGCGGAGGAACGGCGGCGGCGGCAGCTGCAGAGGGCCGACGGCAGCGGAGGAGCGGCGACGGTGGCTGCGAAGGGGCGGT,CGGTGGCAGTTGCGGCGGAGGAACGGTGGCGGCGGTAGCTGCAGAGGGCCAACGGCAGCGGAGGAGCGGCGACGGTGGCTGCGAAGGGGCGGT,CGGTGGCAGTTGCGGCGGAGGAACGGTGGCGGCGGCAGCTGCAGAGGGCCGACGGCAGCGGAGGAGCGGCGACGGTGGCTACGAAGGGGCGGT,CGGTGGCAGTTGCGGCGGAGGAACGGTGGCGGCGGTAGCTGCAGAGGGCCAACGGCAGCGGAGGAGCGGTGACGGTGGCTGCGAAGGGGCGGT]
GGCGGCAGTTGCGGCGGAGGAAAGAGCGACGGCGGCGGCAGCTGCGGAGGGCCGACGGCTGCGGAGGAGCAGCGGCGCTGGGAGCGAAGGGGCGGTGGCG
| Populations | Population Size | Frequency of A(primary allele) | Frequency of ACCGCCCCTTCGCAGCCACC GTCGCCGCTCCTCCGCTGCC ATCAGCCCTCTGCAGCTGCC GCCGCCGCCGTTCCTCCGCC GCAACTGCCACCG(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 49.10% | 2.80% | 2.77% | 43.76% | G: 1.25%; ACCGCCCCTTCGCAGCCACCGTCGCCGCTCCTCCGCTGCCGTTGGCCCTCTGCAGCTACCGCCGCCACCGTTCCTCCGCCGCAACTGCCACCG: 0.13%; ACCGCCCCTTCGCAGCCACCGTCGCCGCTCCTCCGCTGCCGTCGGCCCTCTGCAGCTGCCGCCGCCGCCGTTCCTCCGCCGCAACTGCCACCG: 0.13%; ACCGCCCCTTCGTAGCCACCGTCGCCGCTCCTCCGCTGCCGTCGGCCCTCTGCAGCTGCCGCCGCCACCGTTCCTCCGCCGCAACTGCCACCG: 0.02%; ACCGCCCCTTCGCAGCCACCGTCACCGCTCCTCCGCTGCCGTTGGCCCTCTGCAGCTACCGCCGCCACCGTTCCTCCGCCGCAACTGCCACCG: 0.02% |
| All Indica | 2759 | 50.60% | 4.60% | 4.06% | 38.27% | G: 2.03%; ACCGCCCCTTCGCAGCCACCGTCGCCGCTCCTCCGCTGCCGTCGGCCCTCTGCAGCTGCCGCCGCCGCCGTTCCTCCGCCGCAACTGCCACCG: 0.22%; ACCGCCCCTTCGCAGCCACCGTCGCCGCTCCTCCGCTGCCGTTGGCCCTCTGCAGCTACCGCCGCCACCGTTCCTCCGCCGCAACTGCCACCG: 0.14%; ACCGCCCCTTCGCAGCCACCGTCACCGCTCCTCCGCTGCCGTTGGCCCTCTGCAGCTACCGCCGCCACCGTTCCTCCGCCGCAACTGCCACCG: 0.04% |
| All Japonica | 1512 | 45.40% | 0.20% | 0.60% | 53.64% | G: 0.07%; ACCGCCCCTTCGCAGCCACCGTCGCCGCTCCTCCGCTGCCGTTGGCCCTCTGCAGCTACCGCCGCCACCGTTCCTCCGCCGCAACTGCCACCG: 0.07% |
| Aus | 269 | 49.40% | 0.00% | 0.74% | 49.07% | ACCGCCCCTTCGTAGCCACCGTCGCCGCTCCTCCGCTGCCGTCGGCCCTCTGCAGCTGCCGCCGCCACCGTTCCTCCGCCGCAACTGCCACCG: 0.37%; ACCGCCCCTTCGCAGCCACCGTCGCCGCTCCTCCGCTGCCGTTGGCCCTCTGCAGCTACCGCCGCCACCGTTCCTCCGCCGCAACTGCCACCG: 0.37% |
| Indica I | 595 | 38.20% | 4.90% | 2.35% | 53.11% | G: 1.51% |
| Indica II | 465 | 41.30% | 3.90% | 3.87% | 47.10% | G: 3.87% |
| Indica III | 913 | 61.90% | 5.40% | 5.59% | 24.53% | G: 1.53%; ACCGCCCCTTCGCAGCCACCGTCGCCGCTCCTCCGCTGCCGTCGGCCCTCTGCAGCTGCCGCCGCCGCCGTTCCTCCGCCGCAACTGCCACCG: 0.66%; ACCGCCCCTTCGCAGCCACCGTCGCCGCTCCTCCGCTGCCGTTGGCCCTCTGCAGCTACCGCCGCCACCGTTCCTCCGCCGCAACTGCCACCG: 0.33%; ACCGCCCCTTCGCAGCCACCGTCACCGCTCCTCCGCTGCCGTTGGCCCTCTGCAGCTACCGCCGCCACCGTTCCTCCGCCGCAACTGCCACCG: 0.11% |
| Indica Intermediate | 786 | 52.40% | 4.10% | 3.69% | 37.79% | G: 1.91%; ACCGCCCCTTCGCAGCCACCGTCGCCGCTCCTCCGCTGCCGTTGGCCCTCTGCAGCTACCGCCGCCACCGTTCCTCCGCCGCAACTGCCACCG: 0.13% |
| Temperate Japonica | 767 | 68.70% | 0.30% | 0.65% | 30.25% | G: 0.13% |
| Tropical Japonica | 504 | 17.30% | 0.20% | 0.40% | 82.14% | NA |
| Japonica Intermediate | 241 | 30.30% | 0.00% | 0.83% | 68.46% | ACCGCCCCTTCGCAGCCACCGTCGCCGCTCCTCCGCTGCCGTTGGCCCTCTGCAGCTACCGCCGCCACCGTTCCTCCGCCGCAACTGCCACCG: 0.41% |
| VI/Aromatic | 96 | 52.10% | 2.10% | 5.21% | 38.54% | G: 2.08% |
| Intermediate | 90 | 61.10% | 0.00% | 3.33% | 35.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1208226725 | A -> G | LOC_Os12g14430.1 | downstream_gene_variant ; 2108.0bp to feature; MODIFIER | silent_mutation | Average:61.716; most accessible tissue: Zhenshan97 young leaf, score: 86.852 | N | N | N | N |
| vg1208226725 | A -> G | LOC_Os12g14420-LOC_Os12g14430 | intergenic_region ; MODIFIER | silent_mutation | Average:61.716; most accessible tissue: Zhenshan97 young leaf, score: 86.852 | N | N | N | N |
| vg1208226725 | A -> ACCGCCCCTTCGCAGCCACCGTCGCCGCTC CTCCGCTGCCATCAGCCCTCTGCAGCTGCC GCCGCCGCCGTTCCTCCGCCGCAACTGCCA CCG | LOC_Os12g14430.1 | downstream_gene_variant ; 2107.0bp to feature; MODIFIER | silent_mutation | Average:61.716; most accessible tissue: Zhenshan97 young leaf, score: 86.852 | N | N | N | N |
| vg1208226725 | A -> ACCGCCCCTTCGCAGCCACCGTCGCCGCTC CTCCGCTGCCATCAGCCCTCTGCAGCTGCC GCCGCCGCCGTTCCTCCGCCGCAACTGCCA CCG | LOC_Os12g14420-LOC_Os12g14430 | intergenic_region ; MODIFIER | silent_mutation | Average:61.716; most accessible tissue: Zhenshan97 young leaf, score: 86.852 | N | N | N | N |
| vg1208226725 | A -> ACCGCCCCTTCGCAGCCACCGTCACCGCTC CTCCGCTGCCGTTGGCCCTCTGCAGCTACC GCCGCCACCGTTCCTCCGCCGCAACTGCCA CCG | LOC_Os12g14430.1 | downstream_gene_variant ; 2107.0bp to feature; MODIFIER | silent_mutation | Average:61.716; most accessible tissue: Zhenshan97 young leaf, score: 86.852 | N | N | N | N |
| vg1208226725 | A -> ACCGCCCCTTCGCAGCCACCGTCACCGCTC CTCCGCTGCCGTTGGCCCTCTGCAGCTACC GCCGCCACCGTTCCTCCGCCGCAACTGCCA CCG | LOC_Os12g14420-LOC_Os12g14430 | intergenic_region ; MODIFIER | silent_mutation | Average:61.716; most accessible tissue: Zhenshan97 young leaf, score: 86.852 | N | N | N | N |
| vg1208226725 | A -> ACCGCCCCTTCGCAGCCACCGTCGCCGCTC CTCCGCTGCCGTCGGCCCTCTGCAGCTGCC GCCGCCGCCGTTCCTCCGCCGCAACTGCCA CCG | LOC_Os12g14430.1 | downstream_gene_variant ; 2107.0bp to feature; MODIFIER | silent_mutation | Average:61.716; most accessible tissue: Zhenshan97 young leaf, score: 86.852 | N | N | N | N |
| vg1208226725 | A -> ACCGCCCCTTCGCAGCCACCGTCGCCGCTC CTCCGCTGCCGTCGGCCCTCTGCAGCTGCC GCCGCCGCCGTTCCTCCGCCGCAACTGCCA CCG | LOC_Os12g14420-LOC_Os12g14430 | intergenic_region ; MODIFIER | silent_mutation | Average:61.716; most accessible tissue: Zhenshan97 young leaf, score: 86.852 | N | N | N | N |
| vg1208226725 | A -> ACCGCCCCTTCGCAGCCACCGTCGCCGCTC CTCCGCTGCCGTTGGCCCTCTGCAGCTACC GCCGCCACCGTTCCTCCGCCGCAACTGCCA CCG | LOC_Os12g14430.1 | downstream_gene_variant ; 2107.0bp to feature; MODIFIER | silent_mutation | Average:61.716; most accessible tissue: Zhenshan97 young leaf, score: 86.852 | N | N | N | N |
| vg1208226725 | A -> ACCGCCCCTTCGCAGCCACCGTCGCCGCTC CTCCGCTGCCGTTGGCCCTCTGCAGCTACC GCCGCCACCGTTCCTCCGCCGCAACTGCCA CCG | LOC_Os12g14420-LOC_Os12g14430 | intergenic_region ; MODIFIER | silent_mutation | Average:61.716; most accessible tissue: Zhenshan97 young leaf, score: 86.852 | N | N | N | N |
| vg1208226725 | A -> ACCGCCCCTTCGTAGCCACCGTCGCCGCTC CTCCGCTGCCGTCGGCCCTCTGCAGCTGCC GCCGCCACCGTTCCTCCGCCGCAACTGCCA CCG | LOC_Os12g14430.1 | downstream_gene_variant ; 2107.0bp to feature; MODIFIER | silent_mutation | Average:61.716; most accessible tissue: Zhenshan97 young leaf, score: 86.852 | N | N | N | N |
| vg1208226725 | A -> ACCGCCCCTTCGTAGCCACCGTCGCCGCTC CTCCGCTGCCGTCGGCCCTCTGCAGCTGCC GCCGCCACCGTTCCTCCGCCGCAACTGCCA CCG | LOC_Os12g14420-LOC_Os12g14430 | intergenic_region ; MODIFIER | silent_mutation | Average:61.716; most accessible tissue: Zhenshan97 young leaf, score: 86.852 | N | N | N | N |
| vg1208226725 | A -> DEL | N | N | silent_mutation | Average:61.716; most accessible tissue: Zhenshan97 young leaf, score: 86.852 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1208226725 | NA | 7.01E-06 | mr1011 | 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 |
| vg1208226725 | NA | 4.46E-13 | mr1138 | 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 |
| vg1208226725 | NA | 4.05E-08 | mr1425 | 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 |
| vg1208226725 | NA | 2.17E-06 | mr1577 | 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 |
| vg1208226725 | NA | 7.98E-11 | mr1581 | 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 |
| vg1208226725 | NA | 3.07E-06 | mr1002_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 |
| vg1208226725 | NA | 1.05E-06 | mr1068_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 |
| vg1208226725 | 5.19E-06 | 5.19E-06 | mr1581_2 | 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 |
| vg1208226725 | NA | 6.49E-06 | mr1750_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 |
| vg1208226725 | NA | 1.20E-12 | mr1864_2 | 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 |
| vg1208226725 | NA | 1.90E-10 | mr1864_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 |