| Variant ID: vg1222420009 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 22420009 |
| Reference Allele: T | Alternative Allele: G |
| Primary Allele: T | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
AATGACAGATTAATTAGGCTTAATAGATTCGTCTCGCAGTTTATATGCGGAATTTATAATTTGTTTTGTTATTAGTCTACATTTAATACTTTAAATATGT[T/G]
TCTGTATACTTAAAAAAGATTTGGCACACGAACTAAACACAGCCTAAATAAAGTGCTCAAGAATATACATGAGATTATATTCACAACATTGCCCATTCAG
CTGAATGGGCAATGTTGTGAATATAATCTCATGTATATTCTTGAGCACTTTATTTAGGCTGTGTTTAGTTCGTGTGCCAAATCTTTTTTAAGTATACAGA[A/C]
ACATATTTAAAGTATTAAATGTAGACTAATAACAAAACAAATTATAAATTCCGCATATAAACTGCGAGACGAATCTATTAAGCCTAATTAATCTGTCATT
| Populations | Population Size | Frequency of T(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 24.50% | 18.60% | 1.42% | 55.54% | NA |
| All Indica | 2759 | 3.00% | 14.30% | 2.17% | 80.54% | NA |
| All Japonica | 1512 | 67.70% | 18.80% | 0.33% | 13.23% | NA |
| Aus | 269 | 1.10% | 33.80% | 0.74% | 64.31% | NA |
| Indica I | 595 | 2.40% | 21.30% | 2.35% | 73.95% | NA |
| Indica II | 465 | 3.70% | 1.70% | 2.80% | 91.83% | NA |
| Indica III | 913 | 2.30% | 14.30% | 0.99% | 82.37% | NA |
| Indica Intermediate | 786 | 3.80% | 16.40% | 3.05% | 76.72% | NA |
| Temperate Japonica | 767 | 77.30% | 14.20% | 0.00% | 8.47% | NA |
| Tropical Japonica | 504 | 65.30% | 11.90% | 0.79% | 22.02% | NA |
| Japonica Intermediate | 241 | 41.90% | 47.70% | 0.41% | 9.96% | NA |
| VI/Aromatic | 96 | 8.30% | 87.50% | 0.00% | 4.17% | NA |
| Intermediate | 90 | 45.60% | 25.60% | 0.00% | 28.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1222420009 | T -> DEL | N | N | silent_mutation | Average:11.11; most accessible tissue: Callus, score: 63.722 | N | N | N | N |
| vg1222420009 | T -> G | LOC_Os12g36600.1 | downstream_gene_variant ; 4393.0bp to feature; MODIFIER | silent_mutation | Average:11.11; most accessible tissue: Callus, score: 63.722 | N | N | N | N |
| vg1222420009 | T -> G | LOC_Os12g36610.1 | downstream_gene_variant ; 744.0bp to feature; MODIFIER | silent_mutation | Average:11.11; most accessible tissue: Callus, score: 63.722 | N | N | N | N |
| vg1222420009 | T -> G | LOC_Os12g36620.1 | intron_variant ; MODIFIER | silent_mutation | Average:11.11; most accessible tissue: Callus, score: 63.722 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1222420009 | NA | 2.44E-06 | mr1227_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 |
| vg1222420009 | NA | 1.95E-06 | mr1272_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 |
| vg1222420009 | NA | 1.74E-07 | mr1909_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 |
| vg1222420009 | NA | 2.57E-07 | mr1921_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 |