Variant ID: vg1100321101 (JBrowse) | Variation Type: SNP |
Chromosome: chr11 | Position: 321101 |
Reference Allele: C | Alternative Allele: A |
Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CCGCATAGGCCATCGCAGGGCCCATCCAAACTTCATCACGCCCAGCCTTGCCTGGATGCGTCAGCTAGAGGAAAGCTACACTACAAACCCAGCCGTTGCC[C/A]
ACGCTGGCTTGTGGTAAGCACGATAAATTCTTCTAGGGTTTCCCGCGAACCGGTCCTTAATTGCCATGGGCACGACTAGCAAAACCATGCACCCACATCC
GGATGTGGGTGCATGGTTTTGCTAGTCGTGCCCATGGCAATTAAGGACCGGTTCGCGGGAAACCCTAGAAGAATTTATCGTGCTTACCACAAGCCAGCGT[G/T]
GGCAACGGCTGGGTTTGTAGTGTAGCTTTCCTCTAGCTGACGCATCCAGGCAAGGCTGGGCGTGATGAAGTTTGGATGGGCCCTGCGATGGCCTATGCGG
Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 96.80% | 2.50% | 0.61% | 0.02% | NA |
All Indica | 2759 | 99.00% | 0.80% | 0.14% | 0.04% | NA |
All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Aus | 269 | 56.90% | 33.80% | 9.29% | 0.00% | NA |
Indica I | 595 | 99.80% | 0.00% | 0.00% | 0.17% | NA |
Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica III | 913 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 97.70% | 1.80% | 0.51% | 0.00% | NA |
Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 95.80% | 4.20% | 0.00% | 0.00% | NA |
Intermediate | 90 | 97.80% | 2.20% | 0.00% | 0.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg1100321101 | C -> A | LOC_Os11g01550-LOC_Os11g01570 | intergenic_region ; MODIFIER | silent_mutation | Average:53.699; most accessible tissue: Minghui63 flag leaf, score: 79.676 | N | N | N | N |
vg1100321101 | C -> DEL | N | N | silent_mutation | Average:53.699; most accessible tissue: Minghui63 flag leaf, score: 79.676 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg1100321101 | NA | 5.40E-06 | mr1882_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 |