Search for Variation information by Variation ID:
Detailed information for vg0807248488:
| Variant ID: vg0807248488 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 7248488 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GCCTATTACCTGGGCCCGCTTCACCGCAGCTTTCCGGAGGACCCATGTGCCCGCCGGAGTCATGGCCCTTAAGAAAAGGAAATTCCGAGAGTTGAAGCAA[G/A]
GCAACCGCTCTGTGATGGAGTATTTGCATGAGTTTAACAACCTGGCCCGGTACGCCCCAGAAGATGTTCATGAAGATGAGGAGAAGCAGGAGAAGTTCTT
Reverse complement sequence
AAGAACTTCTCCTGCTTCTCCTCATCTTCATGAACATCTTCTGGGGCGTACCGGGCCAGGTTGTTAAACTCATGCAAATACTCCATCACAGAGCGGTTGC[C/T]
TTGCTTCAACTCTCGGAATTTCCTTTTCTTAAGGGCCATGACTCCGGCGGGCACATGGGTCCTCCGGAAAGCTGCGGTGAAGCGGGCCCAGGTAATAGGC
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 | 70.40% | 2.50% | 10.35% | 16.74% | NA |
| All Indica | 2759 | 54.80% | 0.00% | 17.36% | 27.76% | NA |
| All Japonica | 1512 | 91.30% | 7.80% | 0.20% | 0.66% | NA |
| Aus | 269 | 98.90% | 0.00% | 0.37% | 0.74% | NA |
| Indica I | 595 | 41.00% | 0.20% | 28.91% | 29.92% | NA |
| Indica II | 465 | 73.10% | 0.00% | 10.97% | 15.91% | NA |
| Indica III | 913 | 47.20% | 0.00% | 15.33% | 37.46% | NA |
| Indica Intermediate | 786 | 63.40% | 0.00% | 14.76% | 21.88% | NA |
| Temperate Japonica | 767 | 85.10% | 13.60% | 0.39% | 0.91% | NA |
| Tropical Japonica | 504 | 99.80% | 0.00% | 0.00% | 0.20% | NA |
| Japonica Intermediate | 241 | 93.40% | 5.80% | 0.00% | 0.83% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 78.90% | 1.10% | 5.56% | 14.44% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0807248488 | G -> A | LOC_Os08g12300.1 | missense_variant ; p.Gly644Ser; MODERATE | nonsynonymous_codon ; G644S | Average:28.834; most accessible tissue: Minghui63 young leaf, score: 56.213 | benign  |
0.756 |
DELETERIOUS | 0.01 |
| vg0807248488 | G -> DEL | LOC_Os08g12300.1 | N | frameshift_variant | Average:28.834; most accessible tissue: Minghui63 young leaf, score: 56.213 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0807248488 | NA | 1.39E-06 | mr1648 | 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 |
| vg0807248488 | 7.95E-07 | 7.94E-07 | mr1004_2 | 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 |
| vg0807248488 | NA | 1.81E-06 | mr1051_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 |
| vg0807248488 | NA | 8.73E-06 | mr1631_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 |