| Variant ID: vg1205810984 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 5810984 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CGAAAGGATCGCTTCGCCAGTTGAGACGCTCAAGAAATGGAGCTTCCATTCTCTCTAGATGTGTGGGAAGATGAAAGATGATATGAAGAGCTTGTATTCG[G/A]
CTTGTCTATTATATAGGGCCGCAACTAGTGCTATAACTAGACTTAATTTTGTTCATCTGGCGCACTTGATGTGACAACACGCGCACGCGTGAGCATCATT
AATGATGCTCACGCGTGCGCGTGTTGTCACATCAAGTGCGCCAGATGAACAAAATTAAGTCTAGTTATAGCACTAGTTGCGGCCCTATATAATAGACAAG[C/T]
CGAATACAAGCTCTTCATATCATCTTTCATCTTCCCACACATCTAGAGAGAATGGAAGCTCCATTTCTTGAGCGTCTCAACTGGCGAAGCGATCCTTTCG
| 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 | 82.80% | 3.90% | 9.27% | 4.02% | NA |
| All Indica | 2759 | 83.10% | 3.50% | 11.02% | 2.39% | NA |
| All Japonica | 1512 | 94.30% | 0.10% | 1.52% | 4.10% | NA |
| Aus | 269 | 34.60% | 31.20% | 32.34% | 1.86% | NA |
| Indica I | 595 | 74.60% | 3.20% | 17.48% | 4.71% | NA |
| Indica II | 465 | 94.80% | 0.20% | 3.44% | 1.51% | NA |
| Indica III | 913 | 87.60% | 3.90% | 6.79% | 1.64% | NA |
| Indica Intermediate | 786 | 77.40% | 5.10% | 15.52% | 2.04% | NA |
| Temperate Japonica | 767 | 91.00% | 0.00% | 1.43% | 7.56% | NA |
| Tropical Japonica | 504 | 97.60% | 0.20% | 1.59% | 0.60% | NA |
| Japonica Intermediate | 241 | 97.90% | 0.00% | 1.66% | 0.41% | NA |
| VI/Aromatic | 96 | 27.10% | 2.10% | 18.75% | 52.08% | NA |
| Intermediate | 90 | 83.30% | 2.20% | 6.67% | 7.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1205810984 | G -> DEL | N | N | silent_mutation | Average:10.431; most accessible tissue: Callus, score: 29.984 | N | N | N | N |
| vg1205810984 | G -> A | LOC_Os12g10784.1 | downstream_gene_variant ; 3746.0bp to feature; MODIFIER | silent_mutation | Average:10.431; most accessible tissue: Callus, score: 29.984 | N | N | N | N |
| vg1205810984 | G -> A | LOC_Os12g10784.2 | downstream_gene_variant ; 3746.0bp to feature; MODIFIER | silent_mutation | Average:10.431; most accessible tissue: Callus, score: 29.984 | N | N | N | N |
| vg1205810984 | G -> A | LOC_Os12g10784.3 | downstream_gene_variant ; 3746.0bp to feature; MODIFIER | silent_mutation | Average:10.431; most accessible tissue: Callus, score: 29.984 | N | N | N | N |
| vg1205810984 | G -> A | LOC_Os12g10800.1 | intron_variant ; MODIFIER | silent_mutation | Average:10.431; most accessible tissue: Callus, score: 29.984 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1205810984 | 2.42E-06 | NA | mr1035 | 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 |
| vg1205810984 | 4.64E-06 | NA | mr1626 | 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 |
| vg1205810984 | 4.87E-07 | 1.55E-06 | mr1803 | 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 |