Search for Variation information by Variation ID:
Detailed information for vg0202440501:
| Variant ID: vg0202440501 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 2440501 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 80. )
Flanking Sequence (100 bp) in Reference Genome:
GTGTCGGCTGGTGGAGGCTGCGGCCGGCGACGCGAACCCGGCTAGACGATGGACTGTGGACAGGTCCCTCCTAGCAGCTTTGGTCGATCGATGGAGGCCA[A/G]
AGACGCACACTTTTCACTTGCCGTGCAGTGAGGTAGCCCCTACCCTACAGGACGTATCGTACTTGTTGGGGCTACCGCTCGCGGGAGACGCTGTTGGGCC
Reverse complement sequence
GGCCCAACAGCGTCTCCCGCGAGCGGTAGCCCCAACAAGTACGATACGTCCTGTAGGGTAGGGGCTACCTCACTGCACGGCAAGTGAAAAGTGTGCGTCT[T/C]
TGGCCTCCATCGATCGACCAAAGCTGCTAGGAGGGACCTGTCCACAGTCCATCGTCTAGCCGGGTTCGCGTCGCCGGCCGCAGCCTCCACCAGCCGACAC
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 57.30% | 21.50% | 8.00% | 13.16% | NA |
| All Indica | 2759 | 71.60% | 4.60% | 9.89% | 13.92% | NA |
| All Japonica | 1512 | 42.50% | 56.70% | 0.20% | 0.66% | NA |
| Aus | 269 | 14.50% | 3.30% | 30.86% | 51.30% | NA |
| Indica I | 595 | 96.10% | 0.80% | 0.67% | 2.35% | NA |
| Indica II | 465 | 73.80% | 10.30% | 4.52% | 11.40% | NA |
| Indica III | 913 | 51.80% | 3.20% | 19.82% | 25.19% | NA |
| Indica Intermediate | 786 | 74.80% | 5.60% | 8.52% | 11.07% | NA |
| Temperate Japonica | 767 | 8.60% | 91.40% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 88.70% | 10.10% | 0.40% | 0.79% | NA |
| Japonica Intermediate | 241 | 53.50% | 43.60% | 0.41% | 2.49% | NA |
| VI/Aromatic | 96 | 7.30% | 1.00% | 15.62% | 76.04% | NA |
| Intermediate | 90 | 50.00% | 26.70% | 4.44% | 18.89% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0202440501 | A -> G | LOC_Os02g05110.1 | missense_variant ; p.Lys99Glu; MODERATE | nonsynonymous_codon ; K99E | Average:17.098; most accessible tissue: Callus, score: 40.008 | benign  |
-0.75 |
TOLERATED | 1.00 |
| vg0202440501 | A -> DEL | LOC_Os02g05110.1 | N | frameshift_variant | Average:17.098; most accessible tissue: Callus, score: 40.008 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0202440501 | NA | 3.77E-10 | mr1712 | 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 |
| vg0202440501 | NA | 5.76E-09 | mr1826 | 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 |
| vg0202440501 | NA | 8.75E-06 | mr1910 | 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 |
| vg0202440501 | NA | 6.16E-06 | mr1763_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 |