| Variant ID: vg0624049629 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr06 | Position: 24049629 |
| Reference Allele: T | Alternative Allele: A,TAAAAA,TAAAA,TAAA,TA,TTAA |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TGATCTTTTTTCGGACACGGTGATTTATCCTTTCTGATCATGTTGATGTTGCTCTATCTTCACTATCAATGAAATACTGCAAAGTTCTTCTCTTTTTTTT[T/A,TAAAAA,TAAAA,TAAA,TA,TTAA]
AAAAAAAACAATGATTAGATGGAGTAATTATTTGTATATCCTGTGTGTGTTTTAGGTTCTCGTAGAAGTAGCACGTCAAGAAACTAAGGTCAAAAGTCTT
AAGACTTTTGACCTTAGTTTCTTGACGTGCTACTTCTACGAGAACCTAAAACACACACAGGATATACAAATAATTACTCCATCTAATCATTGTTTTTTTT[A/T,TTTTTA,TTTTA,TTTA,TA,TTAA]
AAAAAAAAGAGAAGAACTTTGCAGTATTTCATTGATAGTGAAGATAGAGCAACATCAACATGATCAGAAAGGATAAATCACCGTGTCCGAAAAAAGATCA
| 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 | 52.60% | 32.30% | 5.23% | 0.00% | TAAAA: 3.81%; TAAA: 2.39%; TA: 2.26%; TAAAAA: 0.95%; TTAA: 0.47% |
| All Indica | 2759 | 68.40% | 9.80% | 5.91% | 0.00% | TAAAA: 6.27%; TAAA: 4.06%; TA: 3.23%; TAAAAA: 1.59%; TTAA: 0.76% |
| All Japonica | 1512 | 35.40% | 59.20% | 4.89% | 0.00% | TA: 0.46%; TAAA: 0.07% |
| Aus | 269 | 5.60% | 92.20% | 0.37% | 0.00% | TA: 0.74%; TAAAA: 0.74%; TTAA: 0.37% |
| Indica I | 595 | 87.90% | 0.70% | 6.22% | 0.00% | TAAAA: 3.03%; TAAAAA: 2.18% |
| Indica II | 465 | 78.90% | 4.30% | 6.67% | 0.00% | TAAAA: 4.95%; TAAA: 2.80%; TAAAAA: 2.15%; TTAA: 0.22% |
| Indica III | 913 | 50.70% | 18.50% | 3.94% | 0.00% | TA: 9.20%; TAAA: 8.43%; TAAAA: 8.00%; TAAAAA: 0.77%; TTAA: 0.44% |
| Indica Intermediate | 786 | 67.80% | 9.90% | 7.51% | 0.00% | TAAAA: 7.51%; TAAA: 2.80%; TTAA: 2.04%; TAAAAA: 1.78%; TA: 0.64% |
| Temperate Japonica | 767 | 13.80% | 79.40% | 6.52% | 0.00% | TA: 0.26% |
| Tropical Japonica | 504 | 76.20% | 19.60% | 3.17% | 0.00% | TA: 0.79%; TAAA: 0.20% |
| Japonica Intermediate | 241 | 18.70% | 77.60% | 3.32% | 0.00% | TA: 0.41% |
| VI/Aromatic | 96 | 5.20% | 88.50% | 0.00% | 0.00% | TA: 6.25% |
| Intermediate | 90 | 50.00% | 30.00% | 10.00% | 0.00% | TAAAA: 5.56%; TA: 3.33%; TAAAAA: 1.11% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0624049629 | T -> TTAA | LOC_Os06g40370.1 | upstream_gene_variant ; 4839.0bp to feature; MODIFIER | silent_mutation | Average:46.293; most accessible tissue: Minghui63 flower, score: 64.685 | N | N | N | N |
| vg0624049629 | T -> TTAA | LOC_Os06g40370-LOC_Os06g40390 | intergenic_region ; MODIFIER | silent_mutation | Average:46.293; most accessible tissue: Minghui63 flower, score: 64.685 | N | N | N | N |
| vg0624049629 | T -> TAAAA | LOC_Os06g40370.1 | upstream_gene_variant ; 4839.0bp to feature; MODIFIER | silent_mutation | Average:46.293; most accessible tissue: Minghui63 flower, score: 64.685 | N | N | N | N |
| vg0624049629 | T -> TAAAA | LOC_Os06g40370-LOC_Os06g40390 | intergenic_region ; MODIFIER | silent_mutation | Average:46.293; most accessible tissue: Minghui63 flower, score: 64.685 | N | N | N | N |
| vg0624049629 | T -> A | LOC_Os06g40370.1 | upstream_gene_variant ; 4838.0bp to feature; MODIFIER | silent_mutation | Average:46.293; most accessible tissue: Minghui63 flower, score: 64.685 | N | N | N | N |
| vg0624049629 | T -> A | LOC_Os06g40370-LOC_Os06g40390 | intergenic_region ; MODIFIER | silent_mutation | Average:46.293; most accessible tissue: Minghui63 flower, score: 64.685 | N | N | N | N |
| vg0624049629 | T -> TAAAAA | LOC_Os06g40370.1 | upstream_gene_variant ; 4839.0bp to feature; MODIFIER | silent_mutation | Average:46.293; most accessible tissue: Minghui63 flower, score: 64.685 | N | N | N | N |
| vg0624049629 | T -> TAAAAA | LOC_Os06g40370-LOC_Os06g40390 | intergenic_region ; MODIFIER | silent_mutation | Average:46.293; most accessible tissue: Minghui63 flower, score: 64.685 | N | N | N | N |
| vg0624049629 | T -> TAAA | LOC_Os06g40370.1 | upstream_gene_variant ; 4839.0bp to feature; MODIFIER | silent_mutation | Average:46.293; most accessible tissue: Minghui63 flower, score: 64.685 | N | N | N | N |
| vg0624049629 | T -> TAAA | LOC_Os06g40370-LOC_Os06g40390 | intergenic_region ; MODIFIER | silent_mutation | Average:46.293; most accessible tissue: Minghui63 flower, score: 64.685 | N | N | N | N |
| vg0624049629 | T -> TA | LOC_Os06g40370.1 | upstream_gene_variant ; 4839.0bp to feature; MODIFIER | silent_mutation | Average:46.293; most accessible tissue: Minghui63 flower, score: 64.685 | N | N | N | N |
| vg0624049629 | T -> TA | LOC_Os06g40370-LOC_Os06g40390 | intergenic_region ; MODIFIER | silent_mutation | Average:46.293; most accessible tissue: Minghui63 flower, score: 64.685 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0624049629 | 1.84E-06 | NA | mr1104 | 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 |
| vg0624049629 | 7.39E-08 | 7.39E-08 | mr1076_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 |
| vg0624049629 | NA | 8.00E-07 | mr1083_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 |