| Variant ID: vg0621437023 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr06 | Position: 21437023 |
| Reference Allele: CAAATTTTTACGT | Alternative Allele: TAAATTTTTACGT,C |
| Primary Allele: CAAATTTTTACGT | Secondary Allele: TAAATTTTTACGT |
Inferred Ancestral Allele: Not determined.
GGTGTTGAGCAGCAGCCCGATGGACACCGACAACAGCGGCGACCTTCAAGACCGCAAAGGCCATGGCGACTGTTATGAAAATAGATGCACAACGGAGACA[CAAATTTTTACGT/TAAATTTTTACGT,C]
GAAAAACCCTTGCGGGAAAAAACCACGAGCGCCGACCGGCAATGATCACTATAGAGGAGATGATTACAAACGTAGGGGAATCACAATGGGAACGTCACCT
AGGTGACGTTCCCATTGTGATTCCCCTACGTTTGTAATCATCTCCTCTATAGTGATCATTGCCGGTCGGCGCTCGTGGTTTTTTCCCGCAAGGGTTTTTC[ACGTAAAAATTTG/ACGTAAAAATTTA,G]
TGTCTCCGTTGTGCATCTATTTTCATAACAGTCGCCATGGCCTTTGCGGTCTTGAAGGTCGCCGCTGTTGTCGGTGTCCATCGGGCTGCTGCTCAACACC
| Populations | Population Size | Frequency of CAAATTTTTACGT(primary allele) | Frequency of TAAATTTTTACGT(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 77.70% | 20.40% | 0.99% | 0.83% | NA |
| All Indica | 2759 | 64.90% | 32.10% | 1.63% | 1.38% | NA |
| All Japonica | 1512 | 95.80% | 4.20% | 0.00% | 0.00% | NA |
| Aus | 269 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica I | 595 | 90.60% | 4.00% | 2.69% | 2.69% | NA |
| Indica II | 465 | 78.70% | 18.90% | 1.29% | 1.08% | NA |
| Indica III | 913 | 41.50% | 56.80% | 1.20% | 0.44% | NA |
| Indica Intermediate | 786 | 64.50% | 32.30% | 1.53% | 1.65% | NA |
| Temperate Japonica | 767 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 89.50% | 10.50% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.30% | 1.70% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 96.90% | 3.10% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 81.10% | 15.60% | 2.22% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0621437023 | CAAATTTTTACGT -> C | LOC_Os06g36490.1 | upstream_gene_variant ; 1322.0bp to feature; MODIFIER | N | Average:68.385; most accessible tissue: Zhenshan97 panicle, score: 85.254 | N | N | N | N |
| vg0621437023 | CAAATTTTTACGT -> C | LOC_Os06g36500.1 | intron_variant ; MODIFIER | N | Average:68.385; most accessible tissue: Zhenshan97 panicle, score: 85.254 | N | N | N | N |
| vg0621437023 | CAAATTTTTACGT -> TAAATTTTTACGT | LOC_Os06g36490.1 | upstream_gene_variant ; 1321.0bp to feature; MODIFIER | silent_mutation | Average:68.385; most accessible tissue: Zhenshan97 panicle, score: 85.254 | N | N | N | N |
| vg0621437023 | CAAATTTTTACGT -> TAAATTTTTACGT | LOC_Os06g36500.1 | intron_variant ; MODIFIER | silent_mutation | Average:68.385; most accessible tissue: Zhenshan97 panicle, score: 85.254 | N | N | N | N |
| vg0621437023 | CAAATTTTTACGT -> DEL | N | N | silent_mutation | Average:68.385; most accessible tissue: Zhenshan97 panicle, score: 85.254 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0621437023 | NA | 2.03E-08 | mr1648 | 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 |
| vg0621437023 | 1.24E-07 | 3.56E-08 | mr1697 | 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 |
| vg0621437023 | 3.51E-06 | 2.00E-06 | mr1697 | Ind_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 |