| Variant ID: vg0910238584 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr09 | Position: 10238584 |
| Reference Allele: A | Alternative Allele: G,AAAAAG,AAAAAAG,AAAAAAAG,AAAAAAAAG,AAAAG |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TTAGGAGAGGTTGTCTAAGATACTCTAGAACATTCACACATTTTCCTTGGGATGTTCTCTACGGTACTCTAGAACATTCCTACTCCCTCCGTCAAAAAAA[A/G,AAAAAG,AAAAAAG,AAAAAAAG,AAAAAAAAG,AAAAG]
ACAAACCATGGTTTCCGTGTCCAACGTTTAACCGTCCGTCTTATTTGAAAAAATTATGAAAAAAATTAAAAAGATAAGTCACGCATAAAATATTAATCAT
ATGATTAATATTTTATGCGTGACTTATCTTTTTAATTTTTTTCATAATTTTTTCAAATAAGACGGACGGTTAAACGTTGGACACGGAAACCATGGTTTGT[T/C,CTTTTT,CTTTTTT,CTTTTTTT,CTTTTTTTT,CTTTT]
TTTTTTTGACGGAGGGAGTAGGAATGTTCTAGAGTACCGTAGAGAACATCCCAAGGAAAATGTGTGAATGTTCTAGAGTATCTTAGACAACCTCTCCTAA
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 40.30% | 35.20% | 3.85% | 13.80% | AAAAAG: 5.33%; AAAAAAAG: 0.80%; AAAAAAG: 0.57%; AAAAG: 0.13%; AAAAAAAAG: 0.04% |
| All Indica | 2759 | 66.00% | 3.80% | 3.95% | 21.75% | AAAAAG: 2.86%; AAAAAAAG: 0.87%; AAAAAAG: 0.69%; AAAAAAAAG: 0.04% |
| All Japonica | 1512 | 0.50% | 92.40% | 4.37% | 1.59% | AAAAAAAG: 0.86%; AAAAAG: 0.13%; AAAAG: 0.07%; AAAAAAAAG: 0.07% |
| Aus | 269 | 19.70% | 8.90% | 1.49% | 4.46% | AAAAAG: 62.08%; AAAAAAG: 1.86%; AAAAG: 1.49% |
| Indica I | 595 | 87.10% | 6.90% | 3.70% | 0.17% | AAAAAG: 1.68%; AAAAAAG: 0.50% |
| Indica II | 465 | 45.40% | 3.70% | 0.86% | 44.73% | AAAAAG: 5.38% |
| Indica III | 913 | 61.30% | 1.90% | 6.13% | 25.85% | AAAAAAAG: 2.30%; AAAAAAG: 1.42%; AAAAAG: 0.99%; AAAAAAAAG: 0.11% |
| Indica Intermediate | 786 | 67.80% | 3.80% | 3.44% | 19.72% | AAAAAG: 4.45%; AAAAAAAG: 0.38%; AAAAAAG: 0.38% |
| Temperate Japonica | 767 | 0.30% | 97.80% | 1.69% | 0.26% | NA |
| Tropical Japonica | 504 | 1.00% | 86.90% | 6.15% | 4.17% | AAAAAAAG: 1.39%; AAAAG: 0.20%; AAAAAG: 0.20% |
| Japonica Intermediate | 241 | 0.40% | 86.70% | 9.13% | 0.41% | AAAAAAAG: 2.49%; AAAAAG: 0.41%; AAAAAAAAG: 0.41% |
| VI/Aromatic | 96 | 4.20% | 83.30% | 2.08% | 6.25% | AAAAAAG: 3.12%; AAAAAG: 1.04% |
| Intermediate | 90 | 20.00% | 62.20% | 1.11% | 11.11% | AAAAAG: 3.33%; AAAAG: 1.11%; AAAAAAAG: 1.11% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0910238584 | A -> AAAAAG | LOC_Os09g16740.1 | upstream_gene_variant ; 3388.0bp to feature; MODIFIER | silent_mutation | Average:37.924; most accessible tissue: Minghui63 panicle, score: 74.563 | N | N | N | N |
| vg0910238584 | A -> AAAAAG | LOC_Os09g16720-LOC_Os09g16740 | intergenic_region ; MODIFIER | silent_mutation | Average:37.924; most accessible tissue: Minghui63 panicle, score: 74.563 | N | N | N | N |
| vg0910238584 | A -> DEL | N | N | silent_mutation | Average:37.924; most accessible tissue: Minghui63 panicle, score: 74.563 | N | N | N | N |
| vg0910238584 | A -> AAAAAAAAG | LOC_Os09g16740.1 | upstream_gene_variant ; 3388.0bp to feature; MODIFIER | silent_mutation | Average:37.924; most accessible tissue: Minghui63 panicle, score: 74.563 | N | N | N | N |
| vg0910238584 | A -> AAAAAAAAG | LOC_Os09g16720-LOC_Os09g16740 | intergenic_region ; MODIFIER | silent_mutation | Average:37.924; most accessible tissue: Minghui63 panicle, score: 74.563 | N | N | N | N |
| vg0910238584 | A -> AAAAAAG | LOC_Os09g16740.1 | upstream_gene_variant ; 3388.0bp to feature; MODIFIER | silent_mutation | Average:37.924; most accessible tissue: Minghui63 panicle, score: 74.563 | N | N | N | N |
| vg0910238584 | A -> AAAAAAG | LOC_Os09g16720-LOC_Os09g16740 | intergenic_region ; MODIFIER | silent_mutation | Average:37.924; most accessible tissue: Minghui63 panicle, score: 74.563 | N | N | N | N |
| vg0910238584 | A -> G | LOC_Os09g16740.1 | upstream_gene_variant ; 3389.0bp to feature; MODIFIER | silent_mutation | Average:37.924; most accessible tissue: Minghui63 panicle, score: 74.563 | N | N | N | N |
| vg0910238584 | A -> G | LOC_Os09g16720-LOC_Os09g16740 | intergenic_region ; MODIFIER | silent_mutation | Average:37.924; most accessible tissue: Minghui63 panicle, score: 74.563 | N | N | N | N |
| vg0910238584 | A -> AAAAG | LOC_Os09g16740.1 | upstream_gene_variant ; 3388.0bp to feature; MODIFIER | silent_mutation | Average:37.924; most accessible tissue: Minghui63 panicle, score: 74.563 | N | N | N | N |
| vg0910238584 | A -> AAAAG | LOC_Os09g16720-LOC_Os09g16740 | intergenic_region ; MODIFIER | silent_mutation | Average:37.924; most accessible tissue: Minghui63 panicle, score: 74.563 | N | N | N | N |
| vg0910238584 | A -> AAAAAAAG | LOC_Os09g16740.1 | upstream_gene_variant ; 3388.0bp to feature; MODIFIER | silent_mutation | Average:37.924; most accessible tissue: Minghui63 panicle, score: 74.563 | N | N | N | N |
| vg0910238584 | A -> AAAAAAAG | LOC_Os09g16720-LOC_Os09g16740 | intergenic_region ; MODIFIER | silent_mutation | Average:37.924; most accessible tissue: Minghui63 panicle, score: 74.563 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0910238584 | NA | 5.30E-13 | mr1362 | 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 |
| vg0910238584 | NA | 7.08E-08 | mr1836 | 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 |
| vg0910238584 | 1.36E-06 | 1.36E-06 | mr1770_2 | Ind_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 |