| Variant ID: vg0602474331 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr06 | Position: 2474331 |
| Reference Allele: CA | Alternative Allele: AA,CAA,C,CAAA |
| Primary Allele: CA | Secondary Allele: AA |
Inferred Ancestral Allele: Not determined.
AACCAAACCTTTATAATTCCATCTTTCTAGATTCATGCTCTCAATTTGTTTAGACAGAGGGCGTGATTTACAAGTCAATCCGTACAGACATTTTCTCTGT[CA/AA,CAA,C,CAAA]
AAAAAAAACCAAATTTCTTGAGATAATAAGCATATTTAGTTTGTGTTTTTTGAAGTTGGTTTTTTTAAACGGAGGATGTAATTTATATGCAACGGCACAT
ATGTGCCGTTGCATATAAATTACATCCTCCGTTTAAAAAAACCAACTTCAAAAAACACAAACTAAATATGCTTATTATCTCAAGAAATTTGGTTTTTTTT[TG/TT,TTG,G,TTTG]
ACAGAGAAAATGTCTGTACGGATTGACTTGTAAATCACGCCCTCTGTCTAAACAAATTGAGAGCATGAATCTAGAAAGATGGAATTATAAAGGTTTGGTT
| Populations | Population Size | Frequency of CA(primary allele) | Frequency of AA(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 87.10% | 4.90% | 2.88% | 2.92% | CAA: 1.84%; C: 0.34%; CAAA: 0.04% |
| All Indica | 2759 | 93.30% | 3.20% | 1.56% | 1.78% | C: 0.07%; CAA: 0.07% |
| All Japonica | 1512 | 88.90% | 0.20% | 4.76% | 0.07% | CAA: 5.56%; C: 0.40%; CAAA: 0.13% |
| Aus | 269 | 9.70% | 49.40% | 6.69% | 32.34% | C: 1.86% |
| Indica I | 595 | 97.30% | 0.30% | 1.51% | 0.84% | NA |
| Indica II | 465 | 98.50% | 0.40% | 0.65% | 0.22% | C: 0.22% |
| Indica III | 913 | 91.60% | 4.90% | 1.75% | 1.53% | CAA: 0.22% |
| Indica Intermediate | 786 | 89.30% | 5.00% | 1.91% | 3.69% | C: 0.13% |
| Temperate Japonica | 767 | 87.10% | 0.10% | 7.56% | 0.00% | CAA: 5.08%; CAAA: 0.13% |
| Tropical Japonica | 504 | 88.10% | 0.00% | 2.18% | 0.20% | CAA: 8.13%; C: 1.19%; CAAA: 0.20% |
| Japonica Intermediate | 241 | 96.30% | 0.80% | 1.24% | 0.00% | CAA: 1.66% |
| VI/Aromatic | 96 | 97.90% | 2.10% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 85.60% | 5.60% | 3.33% | 1.11% | C: 3.33%; CAA: 1.11% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0602474331 | CA -> CAAA | LOC_Os06g05470.1 | downstream_gene_variant ; 927.0bp to feature; MODIFIER | silent_mutation | Average:58.643; most accessible tissue: Minghui63 root, score: 85.669 | N | N | N | N |
| vg0602474331 | CA -> CAAA | LOC_Os06g05480.1 | downstream_gene_variant ; 3159.0bp to feature; MODIFIER | silent_mutation | Average:58.643; most accessible tissue: Minghui63 root, score: 85.669 | N | N | N | N |
| vg0602474331 | CA -> CAAA | LOC_Os06g05470-LOC_Os06g05480 | intergenic_region ; MODIFIER | silent_mutation | Average:58.643; most accessible tissue: Minghui63 root, score: 85.669 | N | N | N | N |
| vg0602474331 | CA -> AA | LOC_Os06g05470.1 | downstream_gene_variant ; 925.0bp to feature; MODIFIER | silent_mutation | Average:58.643; most accessible tissue: Minghui63 root, score: 85.669 | N | N | N | N |
| vg0602474331 | CA -> AA | LOC_Os06g05480.1 | downstream_gene_variant ; 3161.0bp to feature; MODIFIER | silent_mutation | Average:58.643; most accessible tissue: Minghui63 root, score: 85.669 | N | N | N | N |
| vg0602474331 | CA -> AA | LOC_Os06g05470-LOC_Os06g05480 | intergenic_region ; MODIFIER | silent_mutation | Average:58.643; most accessible tissue: Minghui63 root, score: 85.669 | N | N | N | N |
| vg0602474331 | CA -> DEL | N | N | silent_mutation | Average:58.643; most accessible tissue: Minghui63 root, score: 85.669 | N | N | N | N |
| vg0602474331 | CA -> CAA | LOC_Os06g05470.1 | downstream_gene_variant ; 927.0bp to feature; MODIFIER | silent_mutation | Average:58.643; most accessible tissue: Minghui63 root, score: 85.669 | N | N | N | N |
| vg0602474331 | CA -> CAA | LOC_Os06g05480.1 | downstream_gene_variant ; 3159.0bp to feature; MODIFIER | silent_mutation | Average:58.643; most accessible tissue: Minghui63 root, score: 85.669 | N | N | N | N |
| vg0602474331 | CA -> CAA | LOC_Os06g05470-LOC_Os06g05480 | intergenic_region ; MODIFIER | silent_mutation | Average:58.643; most accessible tissue: Minghui63 root, score: 85.669 | N | N | N | N |
| vg0602474331 | CA -> C | LOC_Os06g05470.1 | downstream_gene_variant ; 926.0bp to feature; MODIFIER | silent_mutation | Average:58.643; most accessible tissue: Minghui63 root, score: 85.669 | N | N | N | N |
| vg0602474331 | CA -> C | LOC_Os06g05480.1 | downstream_gene_variant ; 3160.0bp to feature; MODIFIER | silent_mutation | Average:58.643; most accessible tissue: Minghui63 root, score: 85.669 | N | N | N | N |
| vg0602474331 | CA -> C | LOC_Os06g05470-LOC_Os06g05480 | intergenic_region ; MODIFIER | silent_mutation | Average:58.643; most accessible tissue: Minghui63 root, score: 85.669 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0602474331 | 3.36E-06 | NA | mr1141_2 | 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 |
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