| Variant ID: vg0401293916 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 1293916 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GGTCTTCCAAGGACCAATCTGGATATGACTCTATTTGGGTTGTTATCGACCGCCAAACCAAAGTTGCATATTTCATCGCAGTCAAAACCACTTATCCCGG[C/T]
AGTAAGTTGGCAGAATTATACTTTGCTAGGATAGTTTGTCTTCATGGAGTACCGAAGAGAATCGTCTCCGATCGGGGTAGCCAATTCACTACTAAGTTCT
AGAACTTAGTAGTGAATTGGCTACCCCGATCGGAGACGATTCTCTTCGGTACTCCATGAAGACAAACTATCCTAGCAAAGTATAATTCTGCCAACTTACT[G/A]
CCGGGATAAGTGGTTTTGACTGCGATGAAATATGCAACTTTGGTTTGGCGGTCGATAACAACCCAAATAGAGTCATATCCAGATTGGTCCTTGGAAGACC
| 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 | 46.80% | 7.60% | 2.96% | 42.64% | NA |
| All Indica | 2759 | 45.10% | 7.30% | 1.34% | 46.28% | NA |
| All Japonica | 1512 | 55.80% | 1.10% | 0.79% | 42.33% | NA |
| Aus | 269 | 22.70% | 45.40% | 31.60% | 0.37% | NA |
| Indica I | 595 | 74.50% | 0.00% | 0.17% | 25.38% | NA |
| Indica II | 465 | 29.00% | 3.40% | 1.72% | 65.81% | NA |
| Indica III | 913 | 33.70% | 13.90% | 1.31% | 51.04% | NA |
| Indica Intermediate | 786 | 45.50% | 7.40% | 2.04% | 45.04% | NA |
| Temperate Japonica | 767 | 55.90% | 1.30% | 1.17% | 41.59% | NA |
| Tropical Japonica | 504 | 66.70% | 0.20% | 0.20% | 32.94% | NA |
| Japonica Intermediate | 241 | 32.80% | 2.10% | 0.83% | 64.32% | NA |
| VI/Aromatic | 96 | 11.50% | 13.50% | 4.17% | 70.83% | NA |
| Intermediate | 90 | 56.70% | 8.90% | 2.22% | 32.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0401293916 | C -> DEL | LOC_Os04g03110.1 | N | frameshift_variant | Average:13.692; most accessible tissue: Callus, score: 38.569 | N | N | N | N |
| vg0401293916 | C -> T | LOC_Os04g03110.1 | missense_variant&splice_region_variant ; p.Ala1113Val; MODERATE | nonsynonymous_codon ; A1113V | Average:13.692; most accessible tissue: Callus, score: 38.569 | unknown | unknown | TOLERATED | 0.05 |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0401293916 | 2.28E-08 | NA | mr1549 | 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 |
| vg0401293916 | NA | 4.99E-11 | mr1612 | 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 |
| vg0401293916 | 1.58E-07 | 2.20E-36 | mr1757 | 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 |
| vg0401293916 | 2.52E-07 | NA | mr1549_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 |
| vg0401293916 | 6.36E-06 | 8.48E-28 | mr1757_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 |