| Variant ID: vg1126645421 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 26645421 |
| Reference Allele: C | Alternative Allele: A,T |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GTCAGACCAGTCACAGACCGGTCACTCTTGTCCACCACGCGTCAGTTCAGCAAGCTGCATGTCTGCCCTTCTTCATACAATGACTTCCTTGCAATGGTTG[C/A,T]
GATGAAGCCTGGCATATATCTGACCGGGACCGACGTGCCATCTTCAGGAGCTGGCACGCCGTCTCCGGCTAGGGACAAGTGCCTGGAAGCTCTCATCAAT
ATTGATGAGAGCTTCCAGGCACTTGTCCCTAGCCGGAGACGGCGTGCCAGCTCCTGAAGATGGCACGTCGGTCCCGGTCAGATATATGCCAGGCTTCATC[G/T,A]
CAACCATTGCAAGGAAGTCATTGTATGAAGAAGGGCAGACATGCAGCTTGCTGAACTGACGCGTGGTGGACAAGAGTGACCGGTCTGTGACTGGTCTGAC
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 68.80% | 0.60% | 1.97% | 28.67% | T: 0.02% |
| All Indica | 2759 | 66.00% | 0.00% | 1.85% | 32.15% | T: 0.04% |
| All Japonica | 1512 | 76.90% | 1.70% | 1.52% | 19.91% | NA |
| Aus | 269 | 56.50% | 0.00% | 3.35% | 40.15% | NA |
| Indica I | 595 | 84.70% | 0.00% | 0.84% | 14.45% | NA |
| Indica II | 465 | 55.50% | 0.00% | 1.51% | 43.01% | NA |
| Indica III | 913 | 62.00% | 0.00% | 2.85% | 35.16% | NA |
| Indica Intermediate | 786 | 62.60% | 0.00% | 1.65% | 35.62% | T: 0.13% |
| Temperate Japonica | 767 | 89.30% | 0.00% | 0.39% | 10.30% | NA |
| Tropical Japonica | 504 | 58.50% | 5.00% | 2.98% | 33.53% | NA |
| Japonica Intermediate | 241 | 75.50% | 0.40% | 2.07% | 21.99% | NA |
| VI/Aromatic | 96 | 59.40% | 0.00% | 8.33% | 32.29% | NA |
| Intermediate | 90 | 66.70% | 0.00% | 2.22% | 31.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1126645421 | C -> T | LOC_Os11g44130.1 | missense_variant ; p.Ala60Val; MODERATE | nonsynonymous_codon ; A60V | Average:61.081; most accessible tissue: Minghui63 young leaf, score: 81.5 | unknown | unknown | TOLERATED | 0.09 |
| vg1126645421 | C -> A | LOC_Os11g44130.1 | missense_variant ; p.Ala60Glu; MODERATE | nonsynonymous_codon ; A60E | Average:61.081; most accessible tissue: Minghui63 young leaf, score: 81.5 | unknown | unknown | DELETERIOUS | 0.03 |
| vg1126645421 | C -> DEL | LOC_Os11g44130.1 | N | frameshift_variant | Average:61.081; most accessible tissue: Minghui63 young leaf, score: 81.5 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1126645421 | 4.98E-06 | NA | mr1699 | 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 |
| vg1126645421 | 7.47E-08 | 1.07E-08 | mr1699 | 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 |
| vg1126645421 | 6.57E-06 | NA | mr1699_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 |
| vg1126645421 | NA | 1.75E-06 | mr1699_2 | 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 |