Search for Variation information by Variation ID:
Detailed information for vg1105967574:
| Variant ID: vg1105967574 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 5967574 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.57, C: 0.43, others allele: 0.00, population size: 69. )
Flanking Sequence (100 bp) in Reference Genome:
GGTCCTGGTTGTCGAGCGTGAAGAGGAAGGCCATATTCAAAAAGTCCAACGTCCAATTTATTTCGTTAGCGAGGTTTTAGCTGACTCCAAGACAAGATAT[T/C]
CTCAGGTTCAAAAGTTACTATATGGTGTCTTAATTACCGTCAGAAAATTATCTCACTACTTTCAAAGTCACTCGGTCACGGTAGTCACATCGTTTCCACT
Reverse complement sequence
AGTGGAAACGATGTGACTACCGTGACCGAGTGACTTTGAAAGTAGTGAGATAATTTTCTGACGGTAATTAAGACACCATATAGTAACTTTTGAACCTGAG[A/G]
ATATCTTGTCTTGGAGTCAGCTAAAACCTCGCTAACGAAATAAATTGGACGTTGGACTTTTTGAATATGGCCTTCCTCTTCACGCTCGACAACCAGGACC
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 28.40% | 10.20% | 12.67% | 48.73% | NA |
| All Indica | 2759 | 6.30% | 12.90% | 17.51% | 63.28% | NA |
| All Japonica | 1512 | 67.40% | 7.10% | 1.12% | 24.34% | NA |
| Aus | 269 | 10.40% | 0.70% | 31.60% | 57.25% | NA |
| Indica I | 595 | 9.70% | 0.30% | 12.77% | 77.14% | NA |
| Indica II | 465 | 3.40% | 6.90% | 5.59% | 84.09% | NA |
| Indica III | 913 | 3.70% | 22.00% | 28.48% | 45.78% | NA |
| Indica Intermediate | 786 | 8.30% | 15.50% | 15.39% | 60.81% | NA |
| Temperate Japonica | 767 | 66.20% | 0.50% | 1.04% | 32.20% | NA |
| Tropical Japonica | 504 | 65.30% | 18.10% | 1.59% | 15.08% | NA |
| Japonica Intermediate | 241 | 75.50% | 5.40% | 0.41% | 18.67% | NA |
| VI/Aromatic | 96 | 94.80% | 0.00% | 1.04% | 4.17% | NA |
| Intermediate | 90 | 34.40% | 16.70% | 14.44% | 34.44% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1105967574 | T -> DEL | LOC_Os11g10820.1 | N | frameshift_variant | Average:7.917; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |
| vg1105967574 | T -> C | LOC_Os11g10820.1 | missense_variant ; p.Ser1293Pro; MODERATE | nonsynonymous_codon ; S1293P | Average:7.917; most accessible tissue: Minghui63 panicle, score: 20.733 | benign  |
-0.701 |
TOLERATED | 1.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1105967574 | NA | 5.65E-06 | mr1125 | 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 |
| vg1105967574 | 6.87E-07 | 6.87E-07 | mr1144 | Jap_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 |