Variant ID: vg0606407151 (JBrowse) | Variation Type: SNP |
Chromosome: chr06 | Position: 6407151 |
Reference Allele: A | Alternative Allele: C |
Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 309. )
ACTTACTGTGTACATGCACAGGTGATGTTGTGCACAAGAACTATACTAATCCTTGAGACTTCAATCAATTCACATCAACCCCAAGAATTCAACAATATGC[A/C]
TTAACAAAAGACTATTCAATGGAAAAGTATAAAATTTGTTATAGGGCTCTGATGGTGGCAAAGGGATGGAATCCTTTGAGGAGTTCAACTATTCACTCTA
TAGAGTGAATAGTTGAACTCCTCAAAGGATTCCATCCCTTTGCCACCATCAGAGCCCTATAACAAATTTTATACTTTTCCATTGAATAGTCTTTTGTTAA[T/G]
GCATATTGTTGAATTCTTGGGGTTGATGTGAATTGATTGAAGTCTCAAGGATTAGTATAGTTCTTGTGCACAACATCACCTGTGCATGTACACAGTAAGT
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 | 92.10% | 5.50% | 2.41% | 0.00% | NA |
All Indica | 2759 | 98.90% | 0.00% | 1.01% | 0.00% | NA |
All Japonica | 1512 | 77.40% | 17.10% | 5.56% | 0.00% | NA |
Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica I | 595 | 97.30% | 0.00% | 2.69% | 0.00% | NA |
Indica II | 465 | 99.80% | 0.00% | 0.22% | 0.00% | NA |
Indica III | 913 | 99.90% | 0.00% | 0.11% | 0.00% | NA |
Indica Intermediate | 786 | 98.60% | 0.10% | 1.27% | 0.00% | NA |
Temperate Japonica | 767 | 61.00% | 28.90% | 10.04% | 0.00% | NA |
Tropical Japonica | 504 | 98.40% | 1.40% | 0.20% | 0.00% | NA |
Japonica Intermediate | 241 | 85.50% | 12.00% | 2.49% | 0.00% | NA |
VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Intermediate | 90 | 95.60% | 2.20% | 2.22% | 0.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0606407151 | A -> C | LOC_Os06g11990.1 | intron_variant ; MODIFIER | silent_mutation | Average:61.904; most accessible tissue: Minghui63 root, score: 72.958 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0606407151 | 1.41E-06 | NA | mr1310_2 | 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 |
vg0606407151 | NA | 5.39E-08 | mr1681_2 | 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 |
vg0606407151 | 8.79E-07 | 1.97E-13 | mr1959_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 |
vg0606407151 | NA | 2.50E-06 | mr1959_2 | Jap_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 |