| Variant ID: vg0629541634 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr06 | Position: 29541634 |
| Reference Allele: AAAAAG | Alternative Allele: GAAAAG,AGAAAAG,AAGAAAAG,A,AAAGAAAAG |
| Primary Allele: AAAAAG | Secondary Allele: AGAAAAG |
Inferred Ancestral Allele: Not determined.
GATGAGATTATTCTTCGTGGAATATTTTCAGCAGCATTATTTGTCTTTTTAAAAGTTCTAACTGTTCTAATGATTACCTGCTCAGCGTCAAAAAAAAAAA[AAAAAG/GAAAAG,AGAAAAG,AAGAAAAG,A,AAAGAAAAG]
AAGATGACTTGCTTCTTGTTGTTTTTTTTGGGAATTCGCAAGGAGCGCATCTTTATATTAAGAAGAAATAAAGTTTATGTACAAGTGGACATAACAAAAG
CTTTTGTTATGTCCACTTGTACATAAACTTTATTTCTTCTTAATATAAAGATGCGCTCCTTGCGAATTCCCAAAAAAAACAACAAGAAGCAAGTCATCTT[CTTTTT/CTTTTC,CTTTTCT,CTTTTCTT,T,CTTTTCTTT]
TTTTTTTTTTTGACGCTGAGCAGGTAATCATTAGAACAGTTAGAACTTTTAAAAAGACAAATAATGCTGCTGAAAATATTCCACGAAGAATAATCTCATC
| Populations | Population Size | Frequency of AAAAAG(primary allele) | Frequency of AGAAAAG(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 40.20% | 35.40% | 2.31% | 2.88% | GAAAAG: 17.29%; AAGAAAAG: 1.76%; A: 0.11%; AAAGAAAAG: 0.02% |
| All Indica | 2759 | 10.00% | 58.00% | 3.33% | 1.45% | GAAAAG: 24.65%; AAGAAAAG: 2.43%; A: 0.07%; AAAGAAAAG: 0.04% |
| All Japonica | 1512 | 89.80% | 1.20% | 0.79% | 0.07% | GAAAAG: 7.21%; AAGAAAAG: 0.73%; A: 0.20% |
| Aus | 269 | 49.10% | 12.30% | 1.12% | 34.57% | GAAAAG: 1.86%; AAGAAAAG: 1.12% |
| Indica I | 595 | 13.40% | 30.90% | 5.71% | 0.00% | GAAAAG: 45.71%; AAGAAAAG: 4.20% |
| Indica II | 465 | 2.40% | 62.60% | 1.72% | 3.23% | GAAAAG: 30.11% |
| Indica III | 913 | 10.50% | 73.70% | 2.08% | 0.55% | GAAAAG: 11.39%; AAGAAAAG: 1.53%; A: 0.22% |
| Indica Intermediate | 786 | 11.50% | 57.50% | 3.94% | 2.54% | GAAAAG: 20.87%; AAGAAAAG: 3.56%; AAAGAAAAG: 0.13% |
| Temperate Japonica | 767 | 95.60% | 0.80% | 0.91% | 0.00% | GAAAAG: 2.35%; A: 0.39% |
| Tropical Japonica | 504 | 80.00% | 2.00% | 0.99% | 0.00% | GAAAAG: 15.08%; AAGAAAAG: 1.98% |
| Japonica Intermediate | 241 | 92.10% | 0.80% | 0.00% | 0.41% | GAAAAG: 6.22%; AAGAAAAG: 0.41% |
| VI/Aromatic | 96 | 96.90% | 1.00% | 0.00% | 0.00% | GAAAAG: 2.08% |
| Intermediate | 90 | 45.60% | 24.40% | 2.22% | 2.22% | GAAAAG: 23.33%; AAGAAAAG: 2.22% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0629541634 | AAAAAG -> GAAAAG | LOC_Os06g48810.1 | upstream_gene_variant ; 415.0bp to feature; MODIFIER | silent_mutation | Average:66.262; most accessible tissue: Zhenshan97 root, score: 86.026 | N | N | N | N |
| vg0629541634 | AAAAAG -> GAAAAG | LOC_Os06g48810-LOC_Os06g48820 | intergenic_region ; MODIFIER | silent_mutation | Average:66.262; most accessible tissue: Zhenshan97 root, score: 86.026 | N | N | N | N |
| vg0629541634 | AAAAAG -> AAGAAAAG | LOC_Os06g48810.1 | upstream_gene_variant ; 417.0bp to feature; MODIFIER | silent_mutation | Average:66.262; most accessible tissue: Zhenshan97 root, score: 86.026 | N | N | N | N |
| vg0629541634 | AAAAAG -> AAGAAAAG | LOC_Os06g48810-LOC_Os06g48820 | intergenic_region ; MODIFIER | silent_mutation | Average:66.262; most accessible tissue: Zhenshan97 root, score: 86.026 | N | N | N | N |
| vg0629541634 | AAAAAG -> AAAGAAAAG | LOC_Os06g48810.1 | upstream_gene_variant ; 418.0bp to feature; MODIFIER | silent_mutation | Average:66.262; most accessible tissue: Zhenshan97 root, score: 86.026 | N | N | N | N |
| vg0629541634 | AAAAAG -> AAAGAAAAG | LOC_Os06g48810-LOC_Os06g48820 | intergenic_region ; MODIFIER | silent_mutation | Average:66.262; most accessible tissue: Zhenshan97 root, score: 86.026 | N | N | N | N |
| vg0629541634 | AAAAAG -> AGAAAAG | LOC_Os06g48810.1 | upstream_gene_variant ; 416.0bp to feature; MODIFIER | silent_mutation | Average:66.262; most accessible tissue: Zhenshan97 root, score: 86.026 | N | N | N | N |
| vg0629541634 | AAAAAG -> AGAAAAG | LOC_Os06g48810-LOC_Os06g48820 | intergenic_region ; MODIFIER | silent_mutation | Average:66.262; most accessible tissue: Zhenshan97 root, score: 86.026 | N | N | N | N |
| vg0629541634 | AAAAAG -> A | LOC_Os06g48810.1 | upstream_gene_variant ; 416.0bp to feature; MODIFIER | silent_mutation | Average:66.262; most accessible tissue: Zhenshan97 root, score: 86.026 | N | N | N | N |
| vg0629541634 | AAAAAG -> A | LOC_Os06g48810-LOC_Os06g48820 | intergenic_region ; MODIFIER | silent_mutation | Average:66.262; most accessible tissue: Zhenshan97 root, score: 86.026 | N | N | N | N |
| vg0629541634 | AAAAAG -> DEL | N | N | silent_mutation | Average:66.262; most accessible tissue: Zhenshan97 root, score: 86.026 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0629541634 | 2.66E-06 | 9.75E-07 | mr1561 | 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 |
| vg0629541634 | 7.80E-06 | 4.90E-07 | mr1875 | 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 |
| vg0629541634 | NA | 3.54E-06 | mr1908 | 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 |