Search for Variation information by Variation ID:
Detailed information for vg0412733978:
| Variant ID: vg0412733978 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 12733978 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
ATTCCGCATATGGCAAGTTTTTGTCCCAAGCTCCACCAAAATCGAGAGCGCAAGCTCTCAACATATCTTCCAGGATTTGATTGACTCGCTCGGTCTGACC[A/T]
TCAGTTTGCGGGTGATAGGCCGTGCTAAAATTTAAATGGGTCCCCAATTCTTCCTGCAGCTTCTGCCAGAATTTTGAGGTGAACTGACTCCCTCGATCAG
Reverse complement sequence
CTGATCGAGGGAGTCAGTTCACCTCAAAATTCTGGCAGAAGCTGCAGGAAGAATTGGGGACCCATTTAAATTTTAGCACGGCCTATCACCCGCAAACTGA[T/A]
GGTCAGACCGAGCGAGTCAATCAAATCCTGGAAGATATGTTGAGAGCTTGCGCTCTCGATTTTGGTGGAGCTTGGGACAAAAACTTGCCATATGCGGAAT
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 | 36.20% | 1.50% | 44.88% | 17.41% | NA |
| All Indica | 2759 | 3.50% | 2.50% | 66.98% | 27.04% | NA |
| All Japonica | 1512 | 97.90% | 0.00% | 1.85% | 0.26% | NA |
| Aus | 269 | 0.40% | 0.00% | 75.46% | 24.16% | NA |
| Indica I | 595 | 3.20% | 7.20% | 77.98% | 11.60% | NA |
| Indica II | 465 | 4.30% | 1.10% | 65.81% | 28.82% | NA |
| Indica III | 913 | 2.60% | 0.00% | 59.15% | 38.23% | NA |
| Indica Intermediate | 786 | 4.20% | 2.70% | 68.45% | 24.68% | NA |
| Temperate Japonica | 767 | 97.80% | 0.00% | 2.09% | 0.13% | NA |
| Tropical Japonica | 504 | 98.80% | 0.00% | 0.79% | 0.40% | NA |
| Japonica Intermediate | 241 | 96.30% | 0.00% | 3.32% | 0.41% | NA |
| VI/Aromatic | 96 | 88.50% | 0.00% | 10.42% | 1.04% | NA |
| Intermediate | 90 | 56.70% | 0.00% | 35.56% | 7.78% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0412733978 | A -> DEL | LOC_Os04g22490.1 | N | frameshift_variant | Average:12.642; most accessible tissue: Zhenshan97 root, score: 23.888 | N | N | N | N |
| vg0412733978 | A -> T | LOC_Os04g22490.1 | missense_variant ; p.Asp896Glu; MODERATE | nonsynonymous_codon ; D896E | Average:12.642; most accessible tissue: Zhenshan97 root, score: 23.888 | benign  |
1.394 |
DELETERIOUS | 0.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0412733978 | 1.45E-06 | 1.57E-09 | mr1172_2 | 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 |
| vg0412733978 | 2.15E-06 | 3.16E-06 | mr1360_2 | 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 |
| vg0412733978 | 3.11E-06 | 5.09E-06 | mr1360_2 | Ind_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 |
| vg0412733978 | NA | 1.17E-06 | mr1439_2 | 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 |
| vg0412733978 | 4.56E-06 | 3.24E-08 | mr1761_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 |
| vg0412733978 | NA | 5.86E-06 | mr1968_2 | Ind_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 |