Search for Variation information by Variation ID:
Detailed information for vg0307412350:
| Variant ID: vg0307412350 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 7412350 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
AATAATGCATGTATTGGTCTTGCCGTGTTGCGAGACGAGCTTTATTTGTTATCTCTTTCTGAGAATGTGAATGTTGTGTCCTCATTGACAAAAGAAAACA[A/T]
GAAAAGAAAGCGAACTCCCGATGTCTCATCGAAATTATGGCACTATCGTTTGGGCCATATTTCGAGGGGGAGAATTGAGAGACTAGTTAAGAATGAAATT
Reverse complement sequence
AATTTCATTCTTAACTAGTCTCTCAATTCTCCCCCTCGAAATATGGCCCAAACGATAGTGCCATAATTTCGATGAGACATCGGGAGTTCGCTTTCTTTTC[T/A]
TGTTTTCTTTTGTCAATGAGGACACAACATTCACATTCTCAGAAAGAGATAACAAATAAAGCTCGTCTCGCAACACGGCAAGACCAATACATGCATTATT
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 45.70% | 0.30% | 4.74% | 49.26% | NA |
| All Indica | 2759 | 18.10% | 0.50% | 5.73% | 75.68% | NA |
| All Japonica | 1512 | 86.90% | 0.00% | 3.04% | 10.05% | NA |
| Aus | 269 | 72.50% | 0.00% | 6.32% | 21.19% | NA |
| Indica I | 595 | 4.40% | 0.50% | 1.51% | 93.61% | NA |
| Indica II | 465 | 7.70% | 0.20% | 3.23% | 88.82% | NA |
| Indica III | 913 | 34.80% | 0.50% | 10.30% | 54.33% | NA |
| Indica Intermediate | 786 | 15.10% | 0.60% | 5.09% | 79.13% | NA |
| Temperate Japonica | 767 | 82.10% | 0.00% | 1.17% | 16.69% | NA |
| Tropical Japonica | 504 | 89.10% | 0.00% | 7.14% | 3.77% | NA |
| Japonica Intermediate | 241 | 97.50% | 0.00% | 0.41% | 2.07% | NA |
| VI/Aromatic | 96 | 95.80% | 0.00% | 1.04% | 3.12% | NA |
| Intermediate | 90 | 66.70% | 0.00% | 2.22% | 31.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0307412350 | A -> T | LOC_Os03g13700.1 | missense_variant ; p.Lys441Met; MODERATE | nonsynonymous_codon ; K441M | Average:6.822; most accessible tissue: Minghui63 root, score: 17.665 | probably damaging  |
2.373 |
TOLERATED | 0.09 |
| vg0307412350 | A -> DEL | LOC_Os03g13700.1 | N | frameshift_variant | Average:6.822; most accessible tissue: Minghui63 root, score: 17.665 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0307412350 | NA | 2.04E-07 | mr1850 | 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 |
| vg0307412350 | 1.07E-06 | 1.07E-06 | mr1877 | 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 |
| vg0307412350 | 4.67E-07 | 2.49E-08 | mr1090_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 |
| vg0307412350 | NA | 2.98E-06 | mr1211_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 |