| Variant ID: vg1222592221 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 22592221 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TCTTTCTCTATGCTAGATAATATCTCCCACTTAAGTTATCTAGCATGGGTTAATAGTTATCTACTTCCTCCGTTTCAAATTATAAGATGTTTTGACTTTC[G/A]
TCAAAGTCAAATTGCTTCAGTTTTAACTAAGTTTATAGACAAATATAGTAATATTTACATTACTAAATTAGTTTATTAAATTAATAATTAAATATATTTT
AAAATATATTTAATTATTAATTTAATAAACTAATTTAGTAATGTAAATATTACTATATTTGTCTATAAACTTAGTTAAAACTGAAGCAATTTGACTTTGA[C/T]
GAAAGTCAAAACATCTTATAATTTGAAACGGAGGAAGTAGATAACTATTAACCCATGCTAGATAACTTAAGTGGGAGATATTATCTAGCATAGAGAAAGA
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 95.60% | 3.50% | 0.32% | 0.59% | NA |
| All Indica | 2759 | 98.40% | 0.10% | 0.47% | 1.01% | NA |
| All Japonica | 1512 | 93.90% | 6.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 98.80% | 0.30% | 0.67% | 0.17% | NA |
| Indica II | 465 | 96.80% | 0.00% | 1.08% | 2.15% | NA |
| Indica III | 913 | 98.70% | 0.00% | 0.11% | 1.20% | NA |
| Indica Intermediate | 786 | 98.60% | 0.30% | 0.38% | 0.76% | NA |
| Temperate Japonica | 767 | 91.70% | 8.30% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 97.20% | 2.80% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 94.20% | 5.80% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 36.50% | 62.50% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 88.90% | 10.00% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1222592221 | G -> DEL | N | N | silent_mutation | Average:38.072; most accessible tissue: Callus, score: 68.945 | N | N | N | N |
| vg1222592221 | G -> A | LOC_Os12g36860.1 | upstream_gene_variant ; 3148.0bp to feature; MODIFIER | silent_mutation | Average:38.072; most accessible tissue: Callus, score: 68.945 | N | N | N | N |
| vg1222592221 | G -> A | LOC_Os12g36850.1 | intron_variant ; MODIFIER | silent_mutation | Average:38.072; most accessible tissue: Callus, score: 68.945 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1222592221 | 6.07E-07 | NA | Spikelet_length | All | YES | Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652 |
| vg1222592221 | NA | 5.78E-10 | mr1128 | 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 |
| vg1222592221 | NA | 2.77E-08 | mr1829 | 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 |
| vg1222592221 | NA | 7.64E-06 | mr1038_2 | Jap_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 |
| vg1222592221 | 7.07E-06 | 7.07E-06 | mr1389_2 | Jap_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 |
| vg1222592221 | NA | 9.17E-10 | mr1829_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 |