Variant ID: vg0311147041 (JBrowse) | Variation Type: SNP |
Chromosome: chr03 | Position: 11147041 |
Reference Allele: G | Alternative Allele: A |
Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CCCAGGTGAGGTTGGCCGAGGCCCAATAACTTAAGGTTGCCCGGACCCCAACAGTTCATAGGCACACCCACTCGGGGAAAGGCCCAATCTCCAGTTCATA[G/A]
GCACACCCACTCGGGGAAAGGCCCAATCTCCCTAAAAGACTAGTCCGGTAGGGGAAGGGTGGCTCTCCCTTTTAAGGTGGCTTCCTCCTCCCAAGCTAAG
CTTAGCTTGGGAGGAGGAAGCCACCTTAAAAGGGAGAGCCACCCTTCCCCTACCGGACTAGTCTTTTAGGGAGATTGGGCCTTTCCCCGAGTGGGTGTGC[C/T]
TATGAACTGGAGATTGGGCCTTTCCCCGAGTGGGTGTGCCTATGAACTGTTGGGGTCCGGGCAACCTTAAGTTATTGGGCCTCGGCCAACCTCACCTGGG
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 | 95.40% | 3.50% | 1.10% | 0.00% | NA |
All Indica | 2759 | 92.10% | 6.00% | 1.85% | 0.00% | NA |
All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica I | 595 | 93.90% | 1.80% | 4.20% | 0.00% | NA |
Indica II | 465 | 98.30% | 1.50% | 0.22% | 0.00% | NA |
Indica III | 913 | 86.40% | 12.60% | 0.99% | 0.00% | NA |
Indica Intermediate | 786 | 93.80% | 4.20% | 2.04% | 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 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Intermediate | 90 | 97.80% | 1.10% | 1.11% | 0.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0311147041 | G -> A | LOC_Os03g19800.1 | intron_variant ; MODIFIER | silent_mutation | Average:68.857; most accessible tissue: Minghui63 young leaf, score: 80.234 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0311147041 | 9.66E-06 | 9.66E-06 | mr1524 | 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 |
vg0311147041 | 2.93E-06 | 1.43E-06 | mr1671 | Ind_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 |