| Variant ID: vg1219848125 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 19848125 |
| Reference Allele: G | Alternative Allele: T,A |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TTCAAATTAAAATGGTGTCTTTCGTACAAAAACAAAGAGTTTCTTAAACATCAAATAAATATATTTGAAAATTTATAATAGTTAATACTTAGTCAATCTC[G/T,A]
CTAATGAGTTGTCTCATTTTGCGAGGACAGATCAGCTCGGCCGAACAGAATGTTTGAACGCAGCCTAAGTGTCATGATGTGGTCAGTTAGTTGTTTTCGC
GCGAAAACAACTAACTGACCACATCATGACACTTAGGCTGCGTTCAAACATTCTGTTCGGCCGAGCTGATCTGTCCTCGCAAAATGAGACAACTCATTAG[C/A,T]
GAGATTGACTAAGTATTAACTATTATAAATTTTCAAATATATTTATTTGATGTTTAAGAAACTCTTTGTTTTTGTACGAAAGACACCATTTTAATTTGAA
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 91.70% | 7.90% | 0.40% | 0.00% | A: 0.06% |
| All Indica | 2759 | 99.70% | 0.30% | 0.07% | 0.00% | NA |
| All Japonica | 1512 | 80.30% | 18.40% | 1.12% | 0.00% | A: 0.20% |
| Aus | 269 | 72.50% | 27.50% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.50% | 0.20% | 0.34% | 0.00% | NA |
| Indica II | 465 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 67.80% | 29.90% | 1.96% | 0.00% | A: 0.39% |
| Tropical Japonica | 504 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 79.70% | 19.50% | 0.83% | 0.00% | NA |
| VI/Aromatic | 96 | 94.80% | 5.20% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 91.10% | 8.90% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1219848125 | G -> A | LOC_Os12g32850.1 | downstream_gene_variant ; 682.0bp to feature; MODIFIER | silent_mutation | Average:50.384; most accessible tissue: Zhenshan97 young leaf, score: 70.625 | N | N | N | N |
| vg1219848125 | G -> A | LOC_Os12g32840.1 | intron_variant ; MODIFIER | silent_mutation | Average:50.384; most accessible tissue: Zhenshan97 young leaf, score: 70.625 | N | N | N | N |
| vg1219848125 | G -> T | LOC_Os12g32850.1 | downstream_gene_variant ; 682.0bp to feature; MODIFIER | silent_mutation | Average:50.384; most accessible tissue: Zhenshan97 young leaf, score: 70.625 | N | N | N | N |
| vg1219848125 | G -> T | LOC_Os12g32840.1 | intron_variant ; MODIFIER | silent_mutation | Average:50.384; most accessible tissue: Zhenshan97 young leaf, score: 70.625 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1219848125 | 4.07E-06 | 3.82E-10 | Heading_date | All | Not | 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 |
| vg1219848125 | NA | 1.13E-06 | mr1456_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 |
| vg1219848125 | 4.89E-06 | 4.89E-06 | mr1608_2 | Jap_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 |
| vg1219848125 | NA | 3.10E-07 | mr1780_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 |
| vg1219848125 | NA | 4.65E-08 | mr1781_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 |