Search for Variation information by Variation ID:
Detailed information for vg1009825111:
| Variant ID: vg1009825111 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 9825111 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TTGGTTGCAGCCTTAGGTTTGACATAAAGCTTGACTTTCTTGTTGTTGTGGGATGCATGAGGGTTCTTCTTCTGTACCATATTGGCACTAGAACCTCCCT[T/C]
TACCTTTTTGCCCCGGACGTCCTTTGCCCTCGCCTTCTCCTCAACACCCAAAGAGCCAATGAGATCAGAAACACTGAACTCTTGTCTCTTGTGCTTTAGA
Reverse complement sequence
TCTAAAGCACAAGAGACAAGAGTTCAGTGTTTCTGATCTCATTGGCTCTTTGGGTGTTGAGGAGAAGGCGAGGGCAAAGGACGTCCGGGGCAAAAAGGTA[A/G]
AGGGAGGTTCTAGTGCCAATATGGTACAGAAGAAGAACCCTCATGCATCCCACAACAACAAGAAAGTCAAGCTTTATGTCAAACCTAAGGCTGCAACCAA
Allele Frequencies:
| 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 | 26.60% | 12.90% | 18.24% | 42.30% | NA |
| All Indica | 2759 | 32.00% | 1.60% | 6.13% | 60.35% | NA |
| All Japonica | 1512 | 17.00% | 36.40% | 26.59% | 19.97% | NA |
| Aus | 269 | 11.50% | 0.00% | 86.99% | 1.49% | NA |
| Indica I | 595 | 71.30% | 0.50% | 3.53% | 24.71% | NA |
| Indica II | 465 | 15.50% | 1.50% | 3.87% | 79.14% | NA |
| Indica III | 913 | 17.30% | 1.10% | 5.70% | 75.90% | NA |
| Indica Intermediate | 786 | 29.00% | 2.90% | 9.92% | 58.14% | NA |
| Temperate Japonica | 767 | 17.10% | 55.50% | 20.08% | 7.30% | NA |
| Tropical Japonica | 504 | 21.40% | 8.10% | 42.46% | 27.98% | NA |
| Japonica Intermediate | 241 | 7.50% | 34.90% | 14.11% | 43.57% | NA |
| VI/Aromatic | 96 | 65.60% | 0.00% | 32.29% | 2.08% | NA |
| Intermediate | 90 | 25.60% | 16.70% | 28.89% | 28.89% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1009825111 | T -> C | LOC_Os10g19290.1 | missense_variant ; p.Lys349Glu; MODERATE | nonsynonymous_codon ; K349E | Average:17.434; most accessible tissue: Zhenshan97 flag leaf, score: 28.494 | benign  |
-1.487 |
TOLERATED | 1.00 |
| vg1009825111 | T -> DEL | LOC_Os10g19290.1 | N | frameshift_variant | Average:17.434; most accessible tissue: Zhenshan97 flag leaf, score: 28.494 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1009825111 | 8.72E-07 | NA | mr1841 | 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 |
| vg1009825111 | NA | 1.17E-06 | mr1768_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 |
| vg1009825111 | 2.01E-06 | NA | mr1841_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 |