Search for Variation information by Variation ID:
Detailed information for vg1003302040:
| Variant ID: vg1003302040 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 3302040 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
ACGTATTCTGCCACATCTCTCTTCATGTTGGGCCACCAGTATCCTTCCTTCAGATCCTGGTACATCTTCGTACTTCCGGGGTGTAATGAATATGCTGATT[T/C]
GTGAGCTTCCTTTAGAATTAATCCTCTCAGTCCACCCTGTTCAGGTACATAAATCCTCTTTTTATACCATAGGACATCCTTCTCGTCGGTTGAAAATTCC
Reverse complement sequence
GGAATTTTCAACCGACGAGAAGGATGTCCTATGGTATAAAAAGAGGATTTATGTACCTGAACAGGGTGGACTGAGAGGATTAATTCTAAAGGAAGCTCAC[A/G]
AATCAGCATATTCATTACACCCCGGAAGTACGAAGATGTACCAGGATCTGAAGGAAGGATACTGGTGGCCCAACATGAAGAGAGATGTGGCAGAATACGT
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 | 48.30% | 7.40% | 39.36% | 4.87% | NA |
| All Indica | 2759 | 32.10% | 8.30% | 55.74% | 3.81% | NA |
| All Japonica | 1512 | 70.10% | 6.50% | 15.34% | 8.00% | NA |
| Aus | 269 | 86.20% | 3.30% | 10.41% | 0.00% | NA |
| Indica I | 595 | 42.00% | 5.70% | 44.54% | 7.73% | NA |
| Indica II | 465 | 45.60% | 11.80% | 41.08% | 1.51% | NA |
| Indica III | 913 | 18.40% | 8.20% | 72.07% | 1.31% | NA |
| Indica Intermediate | 786 | 32.60% | 8.40% | 53.94% | 5.09% | NA |
| Temperate Japonica | 767 | 70.10% | 5.20% | 22.95% | 1.69% | NA |
| Tropical Japonica | 504 | 70.80% | 6.00% | 5.56% | 17.66% | NA |
| Japonica Intermediate | 241 | 68.50% | 12.00% | 11.62% | 7.88% | NA |
| VI/Aromatic | 96 | 49.00% | 6.20% | 42.71% | 2.08% | NA |
| Intermediate | 90 | 66.70% | 7.80% | 23.33% | 2.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1003302040 | T -> C | LOC_Os10g06430.1 | missense_variant ; p.Lys1154Glu; MODERATE | nonsynonymous_codon ; K1154E | Average:18.929; most accessible tissue: Minghui63 young leaf, score: 26.082 | benign  |
-0.314 |
TOLERATED | 1.00 |
| vg1003302040 | T -> DEL | LOC_Os10g06430.1 | N | frameshift_variant | Average:18.929; most accessible tissue: Minghui63 young leaf, score: 26.082 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1003302040 | 7.27E-08 | 1.16E-08 | mr1698 | 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 |
| vg1003302040 | NA | 2.15E-06 | mr1748 | 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 |
| vg1003302040 | NA | 4.65E-06 | mr1698_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 |