| Variant ID: vg1111313699 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 11313699 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, T: 0.02, others allele: 0.00, population size: 59. )
ATCAGTTCTTGAACTCATTCATGCAGACTCGCAAGGGAACATTGGTTCAGAAGTATAAAGTAAAGGTAGTTGCCGATGATACTGGGACCAGTTCTTCTAA[A/T]
GGTGAAGACGGGAAACAAGCTCTGGACGGCTCGGCGCTACAGACGGTTCTCTAGGAGGTCAAGGTGACAATTCTCAGGGAGTCCATGGGGTTCAAGGTGA
TCACCTTGAACCCCATGGACTCCCTGAGAATTGTCACCTTGACCTCCTAGAGAACCGTCTGTAGCGCCGAGCCGTCCAGAGCTTGTTTCCCGTCTTCACC[T/A]
TTAGAAGAACTGGTCCCAGTATCATCGGCAACTACCTTTACTTTATACTTCTGAACCAATGTTCCCTTGCGAGTCTGCATGAATGAGTTCAAGAACTGAT
| 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 | 39.30% | 4.50% | 51.69% | 4.42% | NA |
| All Indica | 2759 | 9.90% | 7.70% | 76.66% | 5.73% | NA |
| All Japonica | 1512 | 95.40% | 0.00% | 1.79% | 2.78% | NA |
| Aus | 269 | 4.80% | 1.10% | 93.68% | 0.37% | NA |
| Indica I | 595 | 16.10% | 13.80% | 59.66% | 10.42% | NA |
| Indica II | 465 | 10.80% | 4.70% | 78.49% | 6.02% | NA |
| Indica III | 913 | 3.60% | 2.80% | 90.47% | 3.07% | NA |
| Indica Intermediate | 786 | 12.10% | 10.40% | 72.39% | 5.09% | NA |
| Temperate Japonica | 767 | 97.00% | 0.00% | 1.83% | 1.17% | NA |
| Tropical Japonica | 504 | 92.10% | 0.00% | 2.18% | 5.75% | NA |
| Japonica Intermediate | 241 | 97.50% | 0.00% | 0.83% | 1.66% | NA |
| VI/Aromatic | 96 | 89.60% | 0.00% | 10.42% | 0.00% | NA |
| Intermediate | 90 | 47.80% | 0.00% | 43.33% | 8.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1111313699 | A -> T | LOC_Os11g19630.1 | missense_variant&splice_region_variant ; p.Lys92Asn; MODERATE | nonsynonymous_codon ; K92N | Average:25.184; most accessible tissue: Minghui63 root, score: 38.567 | unknown | unknown | DELETERIOUS | 0.01 |
| vg1111313699 | A -> DEL | LOC_Os11g19630.1 | N | frameshift_variant | Average:25.184; most accessible tissue: Minghui63 root, score: 38.567 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1111313699 | NA | 1.78E-07 | mr1321_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 |
| vg1111313699 | 2.34E-07 | NA | mr1686_2 | 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 |
| vg1111313699 | 1.22E-06 | 1.27E-06 | mr1686_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 |