Variant ID: vg0402121041 (JBrowse) | Variation Type: SNP |
Chromosome: chr04 | Position: 2121041 |
Reference Allele: C | Alternative Allele: T |
Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
ACAGATTGTTGCCATTCTTGCGTTTGTGCTATATTTTCCATGAGGTTGTACTGGATCTCTCCTGTCTGCATATCAAGGGTGTCCATTCTCCTAGTGATTT[C/T]
ACCCAAGTCCCAATGAGAGGAACTCGAGCGCCATTTACTTGGAGATGGAGGCACACCACTTGATCTGGAAGGTTGGTTGTCCCCCCCCAATGTATGTCAT
ATGACATACATTGGGGGGGGACAACCAACCTTCCAGATCAAGTGGTGTGCCTCCATCTCCAAGTAAATGGCGCTCGAGTTCCTCTCATTGGGACTTGGGT[G/A]
AAATCACTAGGAGAATGGACACCCTTGATATGCAGACAGGAGAGATCCAGTACAACCTCATGGAAAATATAGCACAAACGCAAGAATGGCAACAATCTGT
Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 27.70% | 5.80% | 7.55% | 58.99% | NA |
All Indica | 2759 | 24.60% | 0.50% | 10.69% | 64.19% | NA |
All Japonica | 1512 | 38.50% | 15.80% | 0.66% | 45.04% | NA |
Aus | 269 | 10.00% | 0.00% | 11.90% | 78.07% | NA |
Indica I | 595 | 24.40% | 0.00% | 15.13% | 60.50% | NA |
Indica II | 465 | 19.40% | 0.00% | 12.47% | 68.17% | NA |
Indica III | 913 | 26.10% | 0.90% | 7.34% | 65.72% | NA |
Indica Intermediate | 786 | 26.20% | 0.80% | 10.18% | 62.85% | NA |
Temperate Japonica | 767 | 68.40% | 19.20% | 0.26% | 12.13% | NA |
Tropical Japonica | 504 | 3.80% | 14.10% | 0.99% | 81.15% | NA |
Japonica Intermediate | 241 | 15.80% | 8.70% | 1.24% | 74.27% | NA |
VI/Aromatic | 96 | 1.00% | 8.30% | 8.33% | 82.29% | NA |
Intermediate | 90 | 22.20% | 12.20% | 13.33% | 52.22% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0402121041 | C -> DEL | LOC_Os04g04460.1 | N | frameshift_variant | Average:8.535; most accessible tissue: Callus, score: 31.61 | N | N | N | N |
vg0402121041 | C -> T | LOC_Os04g04460.1 | missense_variant ; p.Glu72Lys; MODERATE | nonsynonymous_codon ; E72K | Average:8.535; most accessible tissue: Callus, score: 31.61 | benign ![]() |
0.278 ![]() |
TOLERATED | 0.06 |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0402121041 | 8.94E-08 | NA | mr1871_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 |