Variant ID: vg0224549820 (JBrowse) | Variation Type: SNP |
Chromosome: chr02 | Position: 24549820 |
Reference Allele: T | Alternative Allele: C |
Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
GCCTCTAGTCATGATACTCCCGGTCCCATATCACCGACACAAGCAATAACAAGATAAAAGTAATCTGAATTGCAAATAAGAATTAAATACGAATGATAAG[T/C]
TGGGGTTCCGAAGAACAAGCAGACGGACGGTCTAGCCGACACGCGCGCTGCAAGCAAGTAGCAATGGCTAAACTTTAATCTATCAAAACCCAATAAACTG
CAGTTTATTGGGTTTTGATAGATTAAAGTTTAGCCATTGCTACTTGCTTGCAGCGCGCGTGTCGGCTAGACCGTCCGTCTGCTTGTTCTTCGGAACCCCA[A/G]
CTTATCATTCGTATTTAATTCTTATTTGCAATTCAGATTACTTTTATCTTGTTATTGCTTGTGTCGGTGATATGGGACCGGGAGTATCATGACTAGAGGC
Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 9.60% | 4.80% | 2.12% | 83.45% | NA |
All Indica | 2759 | 4.60% | 0.80% | 1.38% | 93.22% | NA |
All Japonica | 1512 | 19.20% | 13.30% | 3.64% | 63.82% | NA |
Aus | 269 | 8.90% | 0.00% | 0.37% | 90.71% | NA |
Indica I | 595 | 1.20% | 0.50% | 0.34% | 97.98% | NA |
Indica II | 465 | 4.70% | 0.40% | 0.65% | 94.19% | NA |
Indica III | 913 | 5.60% | 0.30% | 2.30% | 91.79% | NA |
Indica Intermediate | 786 | 6.10% | 1.70% | 1.53% | 90.71% | NA |
Temperate Japonica | 767 | 22.40% | 16.80% | 3.39% | 57.37% | NA |
Tropical Japonica | 504 | 15.30% | 3.40% | 1.79% | 79.56% | NA |
Japonica Intermediate | 241 | 17.40% | 22.80% | 8.30% | 51.45% | NA |
VI/Aromatic | 96 | 1.00% | 1.00% | 1.04% | 96.88% | NA |
Intermediate | 90 | 12.20% | 4.40% | 5.56% | 77.78% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0224549820 | T -> DEL | N | N | silent_mutation | Average:16.532; most accessible tissue: Minghui63 root, score: 25.504 | N | N | N | N |
vg0224549820 | T -> C | LOC_Os02g40480.1 | upstream_gene_variant ; 1232.0bp to feature; MODIFIER | silent_mutation | Average:16.532; most accessible tissue: Minghui63 root, score: 25.504 | N | N | N | N |
vg0224549820 | T -> C | LOC_Os02g40480-LOC_Os02g40490 | intergenic_region ; MODIFIER | silent_mutation | Average:16.532; most accessible tissue: Minghui63 root, score: 25.504 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0224549820 | 4.45E-06 | 4.45E-06 | mr1910 | 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 |