Variant ID: vg0514548093 (JBrowse) | Variation Type: SNP |
Chromosome: chr05 | Position: 14548093 |
Reference Allele: C | Alternative Allele: T |
Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 120. )
ACGGGTTGAATCAGGATACAATAAAGCATCCTCGATTATAATTTGTGTACCCATTGGGAGTGTAATAGTTGCTCGTCCTGAGCCAACTATCACAGTATCG[C/T]
GCCCAGCGATAGTCAAAACTTTGCCTTCTCTCTTTTTGAGAGTTTGAAAGTATTTGATCTCCCTAAGTATAGAGTTTGTGGTACCACTGTCCACAAGACA
TGTCTTGTGGACAGTGGTACCACAAACTCTATACTTAGGGAGATCAAATACTTTCAAACTCTCAAAAAGAGAGAAGGCAAAGTTTTGACTATCGCTGGGC[G/A]
CGATACTGTGATAGTTGGCTCAGGACGAGCAACTATTACACTCCCAATGGGTACACAAATTATAATCGAGGATGCTTTATTGTATCCTGATTCAACCCGT
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 | 79.90% | 6.30% | 13.01% | 0.83% | NA |
All Indica | 2759 | 69.80% | 9.60% | 19.43% | 1.12% | NA |
All Japonica | 1512 | 99.10% | 0.10% | 0.20% | 0.53% | NA |
Aus | 269 | 66.50% | 11.20% | 22.30% | 0.00% | NA |
Indica I | 595 | 75.80% | 2.00% | 18.82% | 3.36% | NA |
Indica II | 465 | 52.30% | 15.70% | 30.75% | 1.29% | NA |
Indica III | 913 | 75.80% | 10.50% | 13.69% | 0.00% | NA |
Indica Intermediate | 786 | 68.80% | 10.70% | 19.85% | 0.64% | NA |
Temperate Japonica | 767 | 98.60% | 0.30% | 0.26% | 0.91% | NA |
Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 99.20% | 0.00% | 0.41% | 0.41% | NA |
VI/Aromatic | 96 | 99.00% | 0.00% | 1.04% | 0.00% | NA |
Intermediate | 90 | 82.20% | 1.10% | 16.67% | 0.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0514548093 | C -> T | LOC_Os05g25100.1 | upstream_gene_variant ; 4824.0bp to feature; MODIFIER | silent_mutation | Average:8.927; most accessible tissue: Zhenshan97 root, score: 12.891 | N | N | N | N |
vg0514548093 | C -> T | LOC_Os05g25110.1 | intron_variant ; MODIFIER | silent_mutation | Average:8.927; most accessible tissue: Zhenshan97 root, score: 12.891 | N | N | N | N |
vg0514548093 | C -> DEL | N | N | silent_mutation | Average:8.927; most accessible tissue: Zhenshan97 root, score: 12.891 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0514548093 | 3.88E-06 | NA | mr1962_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 |