Variant ID: vg0618221570 (JBrowse) | Variation Type: SNP |
Chromosome: chr06 | Position: 18221570 |
Reference Allele: G | Alternative Allele: A |
Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CCACTAACCCGGAGTCTTGGCTCACCGTCTACAGTCTCGCAATTCGCGCAGCAGGGGGAGACAGCAAAGCCATAGCAAACTACTTGCCTGTGGCTCTAGC[G/A]
GATTCTGCCCGGTCCTGGCTTCATGGGTTACCCCGTGGCACAATCGGATCATGGGCAGAACTTCGCGACCACTTCATCGCCAACTTCTAGGGCACCTTTG
CAAAGGTGCCCTAGAAGTTGGCGATGAAGTGGTCGCGAAGTTCTGCCCATGATCCGATTGTGCCACGGGGTAACCCATGAAGCCAGGACCGGGCAGAATC[C/T]
GCTAGAGCCACAGGCAAGTAGTTTGCTATGGCTTTGCTGTCTCCCCCTGCTGCGCGAATTGCGAGACTGTAGACGGTGAGCCAAGACTCCGGGTTAGTGG
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 | 50.00% | 2.40% | 5.35% | 42.23% | NA |
All Indica | 2759 | 28.20% | 0.20% | 7.76% | 63.83% | NA |
All Japonica | 1512 | 94.30% | 0.20% | 0.26% | 5.22% | NA |
Aus | 269 | 39.80% | 0.40% | 13.01% | 46.84% | NA |
Indica I | 595 | 35.10% | 0.00% | 5.88% | 58.99% | NA |
Indica II | 465 | 39.40% | 0.00% | 8.39% | 52.26% | NA |
Indica III | 913 | 13.60% | 0.20% | 8.54% | 77.66% | NA |
Indica Intermediate | 786 | 33.30% | 0.50% | 7.89% | 58.27% | NA |
Temperate Japonica | 767 | 97.40% | 0.00% | 0.26% | 2.35% | NA |
Tropical Japonica | 504 | 88.30% | 0.00% | 0.40% | 11.31% | NA |
Japonica Intermediate | 241 | 97.10% | 1.20% | 0.00% | 1.66% | NA |
VI/Aromatic | 96 | 2.10% | 95.80% | 0.00% | 2.08% | NA |
Intermediate | 90 | 56.70% | 12.20% | 0.00% | 31.11% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0618221570 | G -> A | LOC_Os06g31310.1 | synonymous_variant ; p.Ala414Ala; LOW | synonymous_codon | Average:8.306; most accessible tissue: Callus, score: 24.524 | N | N | N | N |
vg0618221570 | G -> DEL | LOC_Os06g31310.1 | N | frameshift_variant | Average:8.306; most accessible tissue: Callus, score: 24.524 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0618221570 | NA | 2.68E-07 | mr1438_2 | 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 |
vg0618221570 | NA | 1.35E-06 | mr1994_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 |