Search for Variation information by Variation ID:
Detailed information for vg0403926001:
| Variant ID: vg0403926001 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 3926001 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.86, T: 0.14, others allele: 0.00, population size: 77. )
Flanking Sequence (100 bp) in Reference Genome:
GTGGCGCTTGGGGCGGCAGACCTCTCCCTGGGCGATCTTGAGCTGATGCAGCTGCGCCTCCACTGCGTCTAGGTCCTTCTTGAGCTGCAGGTTCTCCTGA[T/C]
GCAGCTCCAGGATCTTCAAGTTGTTCTCGACCATCCCACGGCGCACCATCTGATGGAAGTCGATACGAGCCGCGTCGTACGCCTCCACCATGCGCGCCAG
Reverse complement sequence
CTGGCGCGCATGGTGGAGGCGTACGACGCGGCTCGTATCGACTTCCATCAGATGGTGCGCCGTGGGATGGTCGAGAACAACTTGAAGATCCTGGAGCTGC[A/G]
TCAGGAGAACCTGCAGCTCAAGAAGGACCTAGACGCAGTGGAGGCGCAGCTGCATCAGCTCAAGATCGCCCAGGGAGAGGTCTGCCGCCCCAAGCGCCAC
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 47.10% | 19.70% | 20.21% | 12.99% | NA |
| All Indica | 2759 | 56.90% | 11.80% | 16.82% | 14.50% | NA |
| All Japonica | 1512 | 31.80% | 35.10% | 20.50% | 12.57% | NA |
| Aus | 269 | 43.90% | 16.40% | 36.06% | 3.72% | NA |
| Indica I | 595 | 17.00% | 26.20% | 26.39% | 30.42% | NA |
| Indica II | 465 | 39.60% | 12.00% | 27.10% | 21.29% | NA |
| Indica III | 913 | 93.10% | 1.30% | 4.38% | 1.20% | NA |
| Indica Intermediate | 786 | 55.30% | 12.80% | 17.94% | 13.87% | NA |
| Temperate Japonica | 767 | 45.40% | 47.60% | 1.43% | 5.61% | NA |
| Tropical Japonica | 504 | 18.10% | 14.70% | 50.00% | 17.26% | NA |
| Japonica Intermediate | 241 | 17.40% | 38.20% | 19.50% | 24.90% | NA |
| VI/Aromatic | 96 | 18.80% | 11.50% | 65.62% | 4.17% | NA |
| Intermediate | 90 | 43.30% | 22.20% | 23.33% | 11.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0403926001 | T -> C | LOC_Os04g07370.1 | missense_variant ; p.His180Arg; MODERATE | nonsynonymous_codon ; H180R | Average:36.406; most accessible tissue: Minghui63 young leaf, score: 74.514 | benign  |
-0.433 |
TOLERATED | 1.00 |
| vg0403926001 | T -> DEL | LOC_Os04g07370.1 | N | frameshift_variant | Average:36.406; most accessible tissue: Minghui63 young leaf, score: 74.514 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0403926001 | 2.94E-06 | NA | mr1023 | 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 |