Variant ID: vg0119798012 (JBrowse) | Variation Type: SNP |
Chromosome: chr01 | Position: 19798012 |
Reference Allele: A | Alternative Allele: C |
Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
CTCACAGCCGGCGGTTGAGTCAACTACCTGGTCAATGCGAGGCAACCCAAAAGGATCTTTGGGGCAAGACTTGTTGAGGTCGGTATAATCAACACACATG[A/C]
GCCATTGCCCTGTTTTCTTCCGAACTAGAACCGGGTTTGCCAGCCAGTCGGGATGAAGGACTTCTTTGATGAAGCCTGCTGCTAACAGCTTGGTTAATTC
GAATTAACCAAGCTGTTAGCAGCAGGCTTCATCAAAGAAGTCCTTCATCCCGACTGGCTGGCAAACCCGGTTCTAGTTCGGAAGAAAACAGGGCAATGGC[T/G]
CATGTGTGTTGATTATACCGACCTCAACAAGTCTTGCCCCAAAGATCCTTTTGGGTTGCCTCGCATTGACCAGGTAGTTGACTCAACCGCCGGCTGTGAG
Populations | Population Size | Frequency of A(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 71.20% | 0.20% | 6.81% | 21.75% | NA |
All Indica | 2759 | 54.20% | 0.30% | 10.69% | 34.76% | NA |
All Japonica | 1512 | 98.80% | 0.00% | 0.60% | 0.60% | NA |
Aus | 269 | 75.50% | 0.00% | 5.95% | 18.59% | NA |
Indica I | 595 | 64.90% | 0.70% | 9.08% | 25.38% | NA |
Indica II | 465 | 73.10% | 0.20% | 7.74% | 18.92% | NA |
Indica III | 913 | 32.60% | 0.10% | 14.02% | 53.23% | NA |
Indica Intermediate | 786 | 60.10% | 0.40% | 9.80% | 29.77% | NA |
Temperate Japonica | 767 | 99.10% | 0.00% | 0.52% | 0.39% | NA |
Tropical Japonica | 504 | 98.80% | 0.00% | 0.60% | 0.60% | NA |
Japonica Intermediate | 241 | 97.90% | 0.00% | 0.83% | 1.24% | NA |
VI/Aromatic | 96 | 99.00% | 0.00% | 0.00% | 1.04% | NA |
Intermediate | 90 | 87.80% | 0.00% | 2.22% | 10.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0119798012 | A -> DEL | LOC_Os01g35740.1 | N | frameshift_variant | Average:17.719; most accessible tissue: Minghui63 young leaf, score: 39.381 | N | N | N | N |
vg0119798012 | A -> C | LOC_Os01g35740.1 | missense_variant ; p.Leu1053Arg; MODERATE | nonsynonymous_codon ; L1053R | Average:17.719; most accessible tissue: Minghui63 young leaf, score: 39.381 | possibly damaging | -1.811 | TOLERATED | 1.00 |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0119798012 | 1.06E-06 | 1.06E-06 | mr1966 | 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 |
vg0119798012 | 4.40E-06 | 4.40E-06 | mr1966 | 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 |