Search for Variation information by Variation ID:
Detailed information for vg0429014530:
| Variant ID: vg0429014530 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 29014530 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
ATTGATAGAGAACATACCCATGAGTATGCCCTGATCTTCCTGGGCCTCTTCAGCTCGGACATGGTTCACTTGTCCGCGCCCAAGTCCAGTGGCGGTCCTG[T/C]
TAGATTGCGGAGTCTTGAATAGACCTCGCCCGGTAACAGGGGTAGTAGTGCCACGAACAGTCATTGCATTCGTGCCGGTCCGGACAGGAGTCTTGCGTGG
Reverse complement sequence
CCACGCAAGACTCCTGTCCGGACCGGCACGAATGCAATGACTGTTCGTGGCACTACTACCCCTGTTACCGGGCGAGGTCTATTCAAGACTCCGCAATCTA[A/G]
CAGGACCGCCACTGGACTTGGGCGCGGACAAGTGAACCATGTCCGAGCTGAAGAGGCCCAGGAAGATCAGGGCATACTCATGGGTATGTTCTCTATCAAT
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 92.70% | 4.40% | 1.42% | 1.48% | NA |
| All Indica | 2759 | 87.60% | 7.50% | 2.39% | 2.54% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 99.60% | 0.00% | 0.37% | 0.00% | NA |
| Indica I | 595 | 68.60% | 21.50% | 4.37% | 5.55% | NA |
| Indica II | 465 | 94.80% | 2.20% | 2.15% | 0.86% | NA |
| Indica III | 913 | 96.30% | 0.70% | 0.99% | 2.08% | NA |
| Indica Intermediate | 786 | 87.50% | 8.00% | 2.67% | 1.78% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0429014530 | T -> C | LOC_Os04g48660.1 | missense_variant ; p.Asn275Ser; MODERATE | nonsynonymous_codon | Average:50.732; most accessible tissue: Minghui63 flag leaf, score: 78.472 | benign  |
1.207 |
TOLERATED | 0.14 |
| vg0429014530 | T -> DEL | LOC_Os04g48660.1 | N | frameshift_variant | Average:50.732; most accessible tissue: Minghui63 flag leaf, score: 78.472 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0429014530 | 2.22E-06 | 1.95E-08 | mr1004 | 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 |
| vg0429014530 | 5.00E-06 | 1.75E-07 | mr1005 | 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 |
| vg0429014530 | NA | 4.58E-07 | mr1011 | 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 |
| vg0429014530 | NA | 4.00E-06 | mr1012 | 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 |