| Variant ID: vg0723509971 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr07 | Position: 23509971 |
| Reference Allele: A | Alternative Allele: T,ATT,ATATT |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.84, T: 0.16, others allele: 0.00, population size: 55. )
AGTATCATTGATGTTATATGTAAAAAAAAAAGTTAATGGTGTGGCCCAATAGCACAAAACCCCAAACCACTCAAGACAAAATATATATATATATATATAT[A/T,ATT,ATATT]
TTAACTAGAGCTAAGAGAAAGACAAAAAAATATCGAGGGCCAAAACTTCTTATACCGAAGAAATAATGTAAGGGTGCTACACTTTGCAATGTTATTTGTA
TACAAATAACATTGCAAAGTGTAGCACCCTTACATTATTTCTTCGGTATAAGAAGTTTTGGCCCTCGATATTTTTTTGTCTTTCTCTTAGCTCTAGTTAA[T/A,AAT,AATAT]
ATATATATATATATATATATTTTGTCTTGAGTGGTTTGGGGTTTTGTGCTATTGGGCCACACCATTAACTTTTTTTTTTACATATAACATCAATGATACT
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 62.20% | 28.90% | 8.08% | 0.00% | ATT: 0.76%; ATATT: 0.04% |
| All Indica | 2759 | 63.00% | 29.90% | 7.07% | 0.00% | ATT: 0.07% |
| All Japonica | 1512 | 59.10% | 28.60% | 10.19% | 0.00% | ATT: 2.05%; ATATT: 0.13% |
| Aus | 269 | 74.70% | 17.80% | 7.43% | 0.00% | NA |
| Indica I | 595 | 85.00% | 3.00% | 11.93% | 0.00% | NA |
| Indica II | 465 | 74.80% | 17.40% | 7.53% | 0.00% | ATT: 0.22% |
| Indica III | 913 | 39.80% | 57.90% | 2.30% | 0.00% | NA |
| Indica Intermediate | 786 | 66.30% | 24.90% | 8.65% | 0.00% | ATT: 0.13% |
| Temperate Japonica | 767 | 86.80% | 7.60% | 4.95% | 0.00% | ATT: 0.65% |
| Tropical Japonica | 504 | 26.60% | 52.80% | 16.27% | 0.00% | ATT: 3.97%; ATATT: 0.40% |
| Japonica Intermediate | 241 | 38.60% | 44.80% | 14.11% | 0.00% | ATT: 2.49% |
| VI/Aromatic | 96 | 64.60% | 33.30% | 0.00% | 0.00% | ATT: 2.08% |
| Intermediate | 90 | 52.20% | 32.20% | 14.44% | 0.00% | ATT: 1.11% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0723509971 | A -> ATATT | LOC_Os07g39270.1 | upstream_gene_variant ; 679.0bp to feature; MODIFIER | silent_mutation | Average:53.728; most accessible tissue: Callus, score: 77.525 | N | N | N | N |
| vg0723509971 | A -> ATATT | LOC_Os07g39270.2 | upstream_gene_variant ; 679.0bp to feature; MODIFIER | silent_mutation | Average:53.728; most accessible tissue: Callus, score: 77.525 | N | N | N | N |
| vg0723509971 | A -> ATATT | LOC_Os07g39280.1 | downstream_gene_variant ; 1927.0bp to feature; MODIFIER | silent_mutation | Average:53.728; most accessible tissue: Callus, score: 77.525 | N | N | N | N |
| vg0723509971 | A -> ATATT | LOC_Os07g39270-LOC_Os07g39280 | intergenic_region ; MODIFIER | silent_mutation | Average:53.728; most accessible tissue: Callus, score: 77.525 | N | N | N | N |
| vg0723509971 | A -> ATT | LOC_Os07g39270.1 | upstream_gene_variant ; 679.0bp to feature; MODIFIER | silent_mutation | Average:53.728; most accessible tissue: Callus, score: 77.525 | N | N | N | N |
| vg0723509971 | A -> ATT | LOC_Os07g39270.2 | upstream_gene_variant ; 679.0bp to feature; MODIFIER | silent_mutation | Average:53.728; most accessible tissue: Callus, score: 77.525 | N | N | N | N |
| vg0723509971 | A -> ATT | LOC_Os07g39280.1 | downstream_gene_variant ; 1927.0bp to feature; MODIFIER | silent_mutation | Average:53.728; most accessible tissue: Callus, score: 77.525 | N | N | N | N |
| vg0723509971 | A -> ATT | LOC_Os07g39270-LOC_Os07g39280 | intergenic_region ; MODIFIER | silent_mutation | Average:53.728; most accessible tissue: Callus, score: 77.525 | N | N | N | N |
| vg0723509971 | A -> T | LOC_Os07g39270.1 | upstream_gene_variant ; 678.0bp to feature; MODIFIER | silent_mutation | Average:53.728; most accessible tissue: Callus, score: 77.525 | N | N | N | N |
| vg0723509971 | A -> T | LOC_Os07g39270.2 | upstream_gene_variant ; 678.0bp to feature; MODIFIER | silent_mutation | Average:53.728; most accessible tissue: Callus, score: 77.525 | N | N | N | N |
| vg0723509971 | A -> T | LOC_Os07g39280.1 | downstream_gene_variant ; 1928.0bp to feature; MODIFIER | silent_mutation | Average:53.728; most accessible tissue: Callus, score: 77.525 | N | N | N | N |
| vg0723509971 | A -> T | LOC_Os07g39270-LOC_Os07g39280 | intergenic_region ; MODIFIER | silent_mutation | Average:53.728; most accessible tissue: Callus, score: 77.525 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0723509971 | NA | 5.87E-06 | mr1080_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 |
| vg0723509971 | 2.55E-06 | NA | mr1563_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 |
| vg0723509971 | NA | 6.91E-08 | mr1563_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 |
| vg0723509971 | NA | 7.15E-06 | mr1594_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 |
| vg0723509971 | 3.95E-06 | 5.08E-10 | mr1865_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 |