| Variant ID: vg1119958713 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr11 | Position: 19958713 |
| Reference Allele: A | Alternative Allele: ATTCTTTGTACAACATTTGTGTGCATTAGAGATTGGACAAAAAGTTACTTACTCTTGCATTCAATC,C,ATTCTTTGTACAACATTTGTGTGCATTAGAGATTGGACAAAAAGTTACTTACTCTTGTATTCAATC,ATTCTTTGTACAACATTTGTGTGCATTAGAGATTGAACAAAAAGTTACTTACTCTTGCATTCAATC,ATTCTTTGTACAACATTTGTGTGTATTAGAGATTGGACAAAAAGTTACTTACTCTTGCATTCAATC |
| Primary Allele: A | Secondary Allele: ATTCTTTGTACAACATTTGT GTGCATTAGAGATTGGACAA AAAGTTACTTACTCTTGCAT TCAATC |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.01, others allele: 0.00, population size: 86. )
ATCTTAGAGACACAAAAAAAAGAGGAAGGGAGGTGCCTTTGCGTTCATAAAAATTTATGGTTATTTGCTTTTTAGTCTCCATTACTTAGTTTCATTCATC[A/ATTCTTTGTACAACATTTGTGTGCATTAGAGATTGGACAAAAAGTTACTTACTCTTGCATTCAATC,C,ATTCTTTGTACAACATTTGTGTGCATTAGAGATTGGACAAAAAGTTACTTACTCTTGTATTCAATC,ATTCTTTGTACAACATTTGTGTGCATTAGAGATTGAACAAAAAGTTACTTACTCTTGCATTCAATC,ATTCTTTGTACAACATTTGTGTGTATTAGAGATTGGACAAAAAGTTACTTACTCTTGCATTCAATC]
TATTCTTTGTACAACATTTGTCCAATCTCTAATAGACTATGTGCATAGACGAAAATGATACACAATAAAAAAACAATGTAAAAATGATCAGTGCTGCATA
TATGCAGCACTGATCATTTTTACATTGTTTTTTTATTGTGTATCATTTTCGTCTATGCACATAGTCTATTAGAGATTGGACAAATGTTGTACAAAGAATA[T/GATTGAATGCAAGAGTAAGTAACTTTTTGTCCAATCTCTAATGCACACAAATGTTGTACAAAGAAT,G,GATTGAATACAAGAGTAAGTAACTTTTTGTCCAATCTCTAATGCACACAAATGTTGTACAAAGAAT,GATTGAATGCAAGAGTAAGTAACTTTTTGTTCAATCTCTAATGCACACAAATGTTGTACAAAGAAT,GATTGAATGCAAGAGTAAGTAACTTTTTGTCCAATCTCTAATACACACAAATGTTGTACAAAGAAT]
GATGAATGAAACTAAGTAATGGAGACTAAAAAGCAAATAACCATAAATTTTTATGAACGCAAAGGCACCTCCCTTCCTCTTTTTTTTGTGTCTCTAAGAT
| Populations | Population Size | Frequency of A(primary allele) | Frequency of ATTCTTTGTACAACATTTGT GTGCATTAGAGATTGGACAA AAAGTTACTTACTCTTGCAT TCAATC(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 40.40% | 38.20% | 5.59% | 8.99% | C: 3.45%; ATTCTTTGTACAACATTTGTGTGCATTAGAGATTGGACAAAAAGTTACTTACTCTTGTATTCAATC: 3.09%; ATTCTTTGTACAACATTTGTGTGCATTAGAGATTGAACAAAAAGTTACTTACTCTTGCATTCAATC: 0.19%; ATTCTTTGTACAACATTTGTGTGTATTAGAGATTGGACAAAAAGTTACTTACTCTTGCATTCAATC: 0.04% |
| All Indica | 2759 | 14.80% | 58.30% | 6.96% | 14.46% | C: 4.89%; ATTCTTTGTACAACATTTGTGTGCATTAGAGATTGGACAAAAAGTTACTTACTCTTGTATTCAATC: 0.54% |
| All Japonica | 1512 | 92.00% | 3.60% | 2.58% | 0.46% | ATTCTTTGTACAACATTTGTGTGCATTAGAGATTGAACAAAAAGTTACTTACTCTTGCATTCAATC: 0.60%; C: 0.46%; ATTCTTTGTACAACATTTGTGTGCATTAGAGATTGGACAAAAAGTTACTTACTCTTGTATTCAATC: 0.13%; ATTCTTTGTACAACATTTGTGTGTATTAGAGATTGGACAAAAAGTTACTTACTCTTGCATTCAATC: 0.13% |
| Aus | 269 | 1.10% | 29.40% | 10.41% | 5.58% | ATTCTTTGTACAACATTTGTGTGCATTAGAGATTGGACAAAAAGTTACTTACTCTTGTATTCAATC: 46.47%; C: 7.06% |
| Indica I | 595 | 10.30% | 69.40% | 7.90% | 8.74% | C: 3.53%; ATTCTTTGTACAACATTTGTGTGCATTAGAGATTGGACAAAAAGTTACTTACTCTTGTATTCAATC: 0.17% |
| Indica II | 465 | 3.00% | 63.40% | 7.31% | 17.85% | C: 7.96%; ATTCTTTGTACAACATTTGTGTGCATTAGAGATTGGACAAAAAGTTACTTACTCTTGTATTCAATC: 0.43% |
| Indica III | 913 | 22.70% | 51.00% | 5.26% | 17.31% | C: 3.40%; ATTCTTTGTACAACATTTGTGTGCATTAGAGATTGGACAAAAAGTTACTTACTCTTGTATTCAATC: 0.33% |
| Indica Intermediate | 786 | 16.20% | 55.30% | 8.02% | 13.49% | C: 5.85%; ATTCTTTGTACAACATTTGTGTGCATTAGAGATTGGACAAAAAGTTACTTACTCTTGTATTCAATC: 1.15% |
| Temperate Japonica | 767 | 93.90% | 4.60% | 0.52% | 0.52% | C: 0.39%; ATTCTTTGTACAACATTTGTGTGCATTAGAGATTGGACAAAAAGTTACTTACTCTTGTATTCAATC: 0.13% |
| Tropical Japonica | 504 | 89.50% | 1.40% | 6.35% | 0.20% | ATTCTTTGTACAACATTTGTGTGCATTAGAGATTGAACAAAAAGTTACTTACTCTTGCATTCAATC: 1.79%; C: 0.79% |
| Japonica Intermediate | 241 | 91.30% | 5.40% | 1.24% | 0.83% | ATTCTTTGTACAACATTTGTGTGTATTAGAGATTGGACAAAAAGTTACTTACTCTTGCATTCAATC: 0.83%; ATTCTTTGTACAACATTTGTGTGCATTAGAGATTGGACAAAAAGTTACTTACTCTTGTATTCAATC: 0.41% |
| VI/Aromatic | 96 | 69.80% | 25.00% | 2.08% | 0.00% | ATTCTTTGTACAACATTTGTGTGCATTAGAGATTGGACAAAAAGTTACTTACTCTTGTATTCAATC: 2.08%; C: 1.04% |
| Intermediate | 90 | 44.40% | 44.40% | 3.33% | 4.44% | ATTCTTTGTACAACATTTGTGTGCATTAGAGATTGGACAAAAAGTTACTTACTCTTGTATTCAATC: 2.22%; C: 1.11% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1119958713 | A -> ATTCTTTGTACAACATTTGTGTGCATTAGA GATTGGACAAAAAGTTACTTACTCTTGCAT TCAATC | LOC_Os11g34100.1 | downstream_gene_variant ; 2869.0bp to feature; MODIFIER | silent_mutation | Average:37.111; most accessible tissue: Minghui63 root, score: 63.193 | N | N | N | N |
| vg1119958713 | A -> ATTCTTTGTACAACATTTGTGTGCATTAGA GATTGGACAAAAAGTTACTTACTCTTGCAT TCAATC | LOC_Os11g34110.1 | intron_variant ; MODIFIER | silent_mutation | Average:37.111; most accessible tissue: Minghui63 root, score: 63.193 | N | N | N | N |
| vg1119958713 | A -> ATTCTTTGTACAACATTTGTGTGCATTAGA GATTGGACAAAAAGTTACTTACTCTTGTAT TCAATC | LOC_Os11g34100.1 | downstream_gene_variant ; 2869.0bp to feature; MODIFIER | silent_mutation | Average:37.111; most accessible tissue: Minghui63 root, score: 63.193 | N | N | N | N |
| vg1119958713 | A -> ATTCTTTGTACAACATTTGTGTGCATTAGA GATTGGACAAAAAGTTACTTACTCTTGTAT TCAATC | LOC_Os11g34110.1 | intron_variant ; MODIFIER | silent_mutation | Average:37.111; most accessible tissue: Minghui63 root, score: 63.193 | N | N | N | N |
| vg1119958713 | A -> ATTCTTTGTACAACATTTGTGTGTATTAGA GATTGGACAAAAAGTTACTTACTCTTGCAT TCAATC | LOC_Os11g34100.1 | downstream_gene_variant ; 2869.0bp to feature; MODIFIER | silent_mutation | Average:37.111; most accessible tissue: Minghui63 root, score: 63.193 | N | N | N | N |
| vg1119958713 | A -> ATTCTTTGTACAACATTTGTGTGTATTAGA GATTGGACAAAAAGTTACTTACTCTTGCAT TCAATC | LOC_Os11g34110.1 | intron_variant ; MODIFIER | silent_mutation | Average:37.111; most accessible tissue: Minghui63 root, score: 63.193 | N | N | N | N |
| vg1119958713 | A -> DEL | N | N | silent_mutation | Average:37.111; most accessible tissue: Minghui63 root, score: 63.193 | N | N | N | N |
| vg1119958713 | A -> ATTCTTTGTACAACATTTGTGTGCATTAGA GATTGAACAAAAAGTTACTTACTCTTGCAT TCAATC | LOC_Os11g34100.1 | downstream_gene_variant ; 2869.0bp to feature; MODIFIER | silent_mutation | Average:37.111; most accessible tissue: Minghui63 root, score: 63.193 | N | N | N | N |
| vg1119958713 | A -> ATTCTTTGTACAACATTTGTGTGCATTAGA GATTGAACAAAAAGTTACTTACTCTTGCAT TCAATC | LOC_Os11g34110.1 | intron_variant ; MODIFIER | silent_mutation | Average:37.111; most accessible tissue: Minghui63 root, score: 63.193 | N | N | N | N |
| vg1119958713 | A -> C | LOC_Os11g34100.1 | downstream_gene_variant ; 2868.0bp to feature; MODIFIER | silent_mutation | Average:37.111; most accessible tissue: Minghui63 root, score: 63.193 | N | N | N | N |
| vg1119958713 | A -> C | LOC_Os11g34110.1 | intron_variant ; MODIFIER | silent_mutation | Average:37.111; most accessible tissue: Minghui63 root, score: 63.193 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1119958713 | 1.29E-06 | 1.29E-06 | mr1497 | 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 |
| vg1119958713 | NA | 1.82E-08 | mr1595 | 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 |
| vg1119958713 | NA | 4.91E-18 | mr1767 | 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 |
| vg1119958713 | NA | 2.37E-07 | mr1921_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 |