Search for Variation information by Variation ID:
Detailed information for vg0401799749:
| Variant ID: vg0401799749 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 1799749 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CTCCAAAACGAGATATCCTCAGGTTCAGAAGCTGTTATACGGTATTCTGATTACTACCAAGAAATTATCCCACTACTTCCAAGGTCACTCGGTAACGGTG[G/A]
TTACATCGTTTCCGCTCGGCGATATACTGCACAACCGCGAAGCAAACGGACGGATTGCTAAATGGGCTTTGGAGTTGATGTCTTTGGACATATCCTTCAA
Reverse complement sequence
TTGAAGGATATGTCCAAAGACATCAACTCCAAAGCCCATTTAGCAATCCGTCCGTTTGCTTCGCGGTTGTGCAGTATATCGCCGAGCGGAAACGATGTAA[C/T]
CACCGTTACCGAGTGACCTTGGAAGTAGTGGGATAATTTCTTGGTAGTAATCAGAATACCGTATAACAGCTTCTGAACCTGAGGATATCTCGTTTTGGAG
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 | 93.50% | 2.40% | 0.55% | 3.55% | NA |
| All Indica | 2759 | 99.80% | 0.10% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 80.20% | 7.10% | 1.65% | 10.98% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.80% | 0.00% | 0.17% | 0.00% | NA |
| Indica II | 465 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 73.30% | 12.50% | 0.52% | 13.69% | NA |
| Tropical Japonica | 504 | 89.30% | 1.20% | 3.57% | 5.95% | NA |
| Japonica Intermediate | 241 | 83.40% | 2.50% | 1.24% | 12.86% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 0.00% | 1.04% | NA |
| Intermediate | 90 | 98.90% | 0.00% | 0.00% | 1.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0401799749 | G -> DEL | LOC_Os04g03940.1 | N | frameshift_variant | Average:39.337; most accessible tissue: Minghui63 flag leaf, score: 60.569 | N | N | N | N |
| vg0401799749 | G -> A | LOC_Os04g03940.1 | missense_variant ; p.Val1255Ile; MODERATE | nonsynonymous_codon ; V1255I | Average:39.337; most accessible tissue: Minghui63 flag leaf, score: 60.569 | benign  |
0.688 |
DELETERIOUS | 0.01 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0401799749 | 4.70E-07 | 4.70E-07 | mr1024_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 |
| vg0401799749 | 3.18E-07 | 2.54E-08 | mr1565_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 |
| vg0401799749 | NA | 1.14E-06 | mr1740_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 |
| vg0401799749 | 5.39E-07 | 5.39E-07 | mr1915_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 |
| vg0401799749 | 5.99E-06 | 1.57E-06 | mr1922_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 |
| vg0401799749 | 4.27E-08 | 4.27E-08 | mr1940_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 |