Search for Variation information by Variation ID:
Detailed information for vg0401440485:
| Variant ID: vg0401440485 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 1440485 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 82. )
Flanking Sequence (100 bp) in Reference Genome:
GGCAATTGAAGCCTCGGAGTCCAGAAAAGAAGATTCCTATAGACCCGGGTGCCAAGAAGTTTTTCAGGAGTATGTCGGCACCAGCCAAGGAGGCCATAAA[G/T]
CTCACGGACTATGAGCGAACACTTAAGAAAGCATATTATGGAAAGTACAAACAAGTCCATCAGCTTGGAGAGCAATCAAACCAGGAGGTCGAGCCATTGG
Reverse complement sequence
CCAATGGCTCGACCTCCTGGTTTGATTGCTCTCCAAGCTGATGGACTTGTTTGTACTTTCCATAATATGCTTTCTTAAGTGTTCGCTCATAGTCCGTGAG[C/A]
TTTATGGCCTCCTTGGCTGGTGCCGACATACTCCTGAAAAACTTCTTGGCACCCGGGTCTATAGGAATCTTCTTTTCTGGACTCCGAGGCTTCAATTGCC
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 47.00% | 5.40% | 45.75% | 1.86% | NA |
| All Indica | 2759 | 46.50% | 3.90% | 49.47% | 0.11% | NA |
| All Japonica | 1512 | 53.10% | 4.80% | 36.57% | 5.56% | NA |
| Aus | 269 | 27.10% | 9.30% | 63.57% | 0.00% | NA |
| Indica I | 595 | 60.30% | 2.20% | 36.97% | 0.50% | NA |
| Indica II | 465 | 54.80% | 2.60% | 42.58% | 0.00% | NA |
| Indica III | 913 | 32.20% | 4.90% | 62.87% | 0.00% | NA |
| Indica Intermediate | 786 | 47.80% | 4.70% | 47.46% | 0.00% | NA |
| Temperate Japonica | 767 | 75.60% | 0.50% | 13.17% | 10.69% | NA |
| Tropical Japonica | 504 | 23.00% | 10.50% | 66.27% | 0.20% | NA |
| Japonica Intermediate | 241 | 44.40% | 6.20% | 48.96% | 0.41% | NA |
| VI/Aromatic | 96 | 14.60% | 47.90% | 37.50% | 0.00% | NA |
| Intermediate | 90 | 51.10% | 6.70% | 41.11% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0401440485 | G -> DEL | LOC_Os04g03350.1 | N | frameshift_variant | Average:15.371; most accessible tissue: Callus, score: 43.949 | N | N | N | N |
| vg0401440485 | G -> T | LOC_Os04g03350.1 | missense_variant ; p.Lys475Asn; MODERATE | nonsynonymous_codon ; K475N | Average:15.371; most accessible tissue: Callus, score: 43.949 | possibly damaging  |
1.714 |
DELETERIOUS | 0.01 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0401440485 | 3.99E-06 | 3.99E-06 | mr1529_2 | Ind_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 |