Search for Variation information by Variation ID:
Detailed information for vg1000477621:
| Variant ID: vg1000477621 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 477621 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 86. )
Flanking Sequence (100 bp) in Reference Genome:
CCTACGTGAGGATCCCTCTCCTCTCTCAAACCGCGTTTTAGTAACCCTGTATTGCTCTGGTAGTTCAAGCTGCACAACACGGCTAGGTGGAGTTAGCACC[C/T]
TTCTGGTGTCTATCCATTCTCTGTATTGACATCTCCTTGGTGGTTCCTGGGAGAAAAGAATAGATGTGAAGCGAGCAAAGTTAGTAAATGTTGTGAGAAA
Reverse complement sequence
TTTCTCACAACATTTACTAACTTTGCTCGCTTCACATCTATTCTTTTCTCCCAGGAACCACCAAGGAGATGTCAATACAGAGAATGGATAGACACCAGAA[G/A]
GGTGCTAACTCCACCTAGCCGTGTTGTGCAGCTTGAACTACCAGAGCAATACAGGGTTACTAAAACGCGGTTTGAGAGAGGAGAGGGATCCTCACGTAGG
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 | 76.00% | 16.00% | 0.32% | 7.62% | NA |
| All Indica | 2759 | 69.30% | 26.40% | 0.33% | 3.99% | NA |
| All Japonica | 1512 | 98.40% | 1.00% | 0.07% | 0.53% | NA |
| Aus | 269 | 27.50% | 0.00% | 1.49% | 71.00% | NA |
| Indica I | 595 | 80.30% | 19.30% | 0.34% | 0.00% | NA |
| Indica II | 465 | 53.10% | 45.60% | 0.22% | 1.08% | NA |
| Indica III | 913 | 73.80% | 19.50% | 0.33% | 6.35% | NA |
| Indica Intermediate | 786 | 65.10% | 28.50% | 0.38% | 5.98% | NA |
| Temperate Japonica | 767 | 99.50% | 0.40% | 0.00% | 0.13% | NA |
| Tropical Japonica | 504 | 98.20% | 1.60% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 95.40% | 1.70% | 0.00% | 2.90% | NA |
| VI/Aromatic | 96 | 54.20% | 3.10% | 0.00% | 42.71% | NA |
| Intermediate | 90 | 75.60% | 12.20% | 1.11% | 11.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1000477621 | C -> T | LOC_Os10g01740.1 | missense_variant ; p.Arg17Lys; MODERATE | nonsynonymous_codon ; R17K | Average:19.991; most accessible tissue: Minghui63 panicle, score: 29.741 | benign  |
0.11 |
TOLERATED | 0.11 |
| vg1000477621 | C -> DEL | LOC_Os10g01740.1 | N | frameshift_variant | Average:19.991; most accessible tissue: Minghui63 panicle, score: 29.741 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1000477621 | NA | 1.58E-08 | mr1709 | 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 |
| vg1000477621 | NA | 1.13E-06 | mr1709 | Ind_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 |
| vg1000477621 | NA | 3.86E-09 | mr1709_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 |
| vg1000477621 | NA | 2.81E-08 | mr1709_2 | Ind_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 |