| Variant ID: vg1222419797 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 22419797 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GACAAGACAATATACTAGAAATATCAACATTTTAGGCCAAGTTTAGTTCCAAAATTTTTCTTCAAACTTTCAACTTTTTCATCACATCAAAACTTTCCTA[C/T]
ACACACAAATTTCCAACTTTTCCGTCACATCATTCCAATTTTAACCAAATTTCTAATTTTGGCGTTGATTTGATATGATTTGACAATGTGATGCTACCGT
ACGGTAGCATCACATTGTCAAATCATATCAAATCAACGCCAAAATTAGAAATTTGGTTAAAATTGGAATGATGTGACGGAAAAGTTGGAAATTTGTGTGT[G/A]
TAGGAAAGTTTTGATGTGATGAAAAAGTTGAAAGTTTGAAGAAAAATTTTGGAACTAAACTTGGCCTAAAATGTTGATATTTCTAGTATATTGTCTTGTC
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 52.00% | 4.70% | 0.38% | 42.93% | NA |
| All Indica | 2759 | 32.40% | 7.40% | 0.47% | 59.73% | NA |
| All Japonica | 1512 | 86.60% | 0.30% | 0.07% | 13.10% | NA |
| Aus | 269 | 35.70% | 3.30% | 1.49% | 59.48% | NA |
| Indica I | 595 | 29.60% | 12.40% | 0.50% | 57.48% | NA |
| Indica II | 465 | 21.90% | 1.30% | 0.22% | 76.56% | NA |
| Indica III | 913 | 39.50% | 5.70% | 0.44% | 54.33% | NA |
| Indica Intermediate | 786 | 32.40% | 9.20% | 0.64% | 57.76% | NA |
| Temperate Japonica | 767 | 91.30% | 0.10% | 0.13% | 8.47% | NA |
| Tropical Japonica | 504 | 78.40% | 0.00% | 0.00% | 21.63% | NA |
| Japonica Intermediate | 241 | 88.80% | 1.20% | 0.00% | 9.96% | NA |
| VI/Aromatic | 96 | 92.70% | 2.10% | 0.00% | 5.21% | NA |
| Intermediate | 90 | 76.70% | 3.30% | 0.00% | 20.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1222419797 | C -> DEL | N | N | silent_mutation | Average:9.666; most accessible tissue: Callus, score: 56.791 | N | N | N | N |
| vg1222419797 | C -> T | LOC_Os12g36620.1 | splice_region_variant&intron_variant ; LOW | silent_mutation | Average:9.666; most accessible tissue: Callus, score: 56.791 | N | N | N | N |
| vg1222419797 | C -> T | LOC_Os12g36600.1 | downstream_gene_variant ; 4181.0bp to feature; MODIFIER | silent_mutation | Average:9.666; most accessible tissue: Callus, score: 56.791 | N | N | N | N |
| vg1222419797 | C -> T | LOC_Os12g36610.1 | downstream_gene_variant ; 532.0bp to feature; MODIFIER | silent_mutation | Average:9.666; most accessible tissue: Callus, score: 56.791 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1222419797 | NA | 4.34E-07 | mr1021 | 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 |
| vg1222419797 | NA | 2.54E-06 | mr1677 | 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 |
| vg1222419797 | NA | 2.36E-06 | mr1677 | 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 |
| vg1222419797 | NA | 4.60E-07 | mr1990 | 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 |