Variant ID: vg1102590535 (JBrowse) | Variation Type: SNP |
Chromosome: chr11 | Position: 2590535 |
Reference Allele: C | Alternative Allele: T |
Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GAAATTAAAGCAATGTCACGAAAATATTGAAAGTTTGTGTGTAGAATAATTTTTATGTGATGGAAAAGTTGGAAGTTTAAAGAAAAAGTTTGGAACTAAA[C/T]
TCGGCCCTGGTTGACAGCAAACTTTTAAAAATATAGTGAAGTTGAATTTTTCACCTTTTAATTTCTAGCTACGCCGTGTTTAGTTTCAAAATAATTCTTC
GAAGAATTATTTTGAAACTAAACACGGCGTAGCTAGAAATTAAAAGGTGAAAAATTCAACTTCACTATATTTTTAAAAGTTTGCTGTCAACCAGGGCCGA[G/A]
TTTAGTTCCAAACTTTTTCTTTAAACTTCCAACTTTTCCATCACATAAAAATTATTCTACACACAAACTTTCAATATTTTCGTGACATTGCTTTAATTTC
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 | 56.00% | 6.60% | 9.94% | 27.47% | NA |
All Indica | 2759 | 29.20% | 11.10% | 15.66% | 44.00% | NA |
All Japonica | 1512 | 99.20% | 0.20% | 0.00% | 0.60% | NA |
Aus | 269 | 65.80% | 0.40% | 11.15% | 22.68% | NA |
Indica I | 595 | 67.40% | 14.30% | 7.90% | 10.42% | NA |
Indica II | 465 | 9.50% | 8.00% | 6.45% | 76.13% | NA |
Indica III | 913 | 12.30% | 6.90% | 26.62% | 54.22% | NA |
Indica Intermediate | 786 | 31.80% | 15.40% | 14.25% | 38.55% | NA |
Temperate Japonica | 767 | 99.00% | 0.30% | 0.00% | 0.78% | NA |
Tropical Japonica | 504 | 99.60% | 0.00% | 0.00% | 0.40% | NA |
Japonica Intermediate | 241 | 99.20% | 0.40% | 0.00% | 0.41% | NA |
VI/Aromatic | 96 | 99.00% | 0.00% | 1.04% | 0.00% | NA |
Intermediate | 90 | 74.40% | 2.20% | 7.78% | 15.56% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg1102590535 | C -> T | LOC_Os11g05680-LOC_Os11g05690 | intergenic_region ; MODIFIER | silent_mutation | Average:46.714; most accessible tissue: Callus, score: 90.843 | N | N | N | N |
vg1102590535 | C -> DEL | N | N | silent_mutation | Average:46.714; most accessible tissue: Callus, score: 90.843 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg1102590535 | 4.52E-10 | 3.69E-12 | mr1397 | 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 |