Search for Variation information by Variation ID:
Detailed information for vg1021960509:
| Variant ID: vg1021960509 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 21960509 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, A: 0.01, others allele: 0.00, population size: 200. )
Flanking Sequence (100 bp) in Reference Genome:
ACTTCCACTTCCAAGATCATCCTAAATGGTACACCGGGAGAGGCAATAAGGCACGGAAAAGGCTTACGACAAGGCGACCCCTTATCTCCATTGCTCTTCA[T/A]
TCTAGCAATCGACCCACTCCAGCGCCTTTTGGACAAGGCCACTGATCTAGGGGCGATAAGTAAACTGAGAGGAAGGGTTATTTGCTTCCGCACATCCATG
Reverse complement sequence
CATGGATGTGCGGAAGCAAATAACCCTTCCTCTCAGTTTACTTATCGCCCCTAGATCAGTGGCCTTGTCCAAAAGGCGCTGGAGTGGGTCGATTGCTAGA[A/T]
TGAAGAGCAATGGAGATAAGGGGTCGCCTTGTCGTAAGCCTTTTCCGTGCCTTATTGCCTCTCCCGGTGTACCATTTAGGATGATCTTGGAAGTGGAAGT
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 92.50% | 6.00% | 1.52% | 0.00% | NA |
| All Indica | 2759 | 98.20% | 1.50% | 0.33% | 0.00% | NA |
| All Japonica | 1512 | 90.10% | 6.80% | 3.11% | 0.00% | NA |
| Aus | 269 | 47.20% | 48.70% | 4.09% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.10% | 0.00% | 0.86% | 0.00% | NA |
| Indica III | 913 | 98.60% | 1.40% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 95.80% | 3.60% | 0.64% | 0.00% | NA |
| Temperate Japonica | 767 | 95.30% | 0.90% | 3.78% | 0.00% | NA |
| Tropical Japonica | 504 | 85.70% | 12.90% | 1.39% | 0.00% | NA |
| Japonica Intermediate | 241 | 82.60% | 12.90% | 4.56% | 0.00% | NA |
| VI/Aromatic | 96 | 95.80% | 2.10% | 2.08% | 0.00% | NA |
| Intermediate | 90 | 88.90% | 7.80% | 3.33% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1021960509 | T -> A | LOC_Os10g40840.1 | missense_variant ; p.Ile367Asn; MODERATE | nonsynonymous_codon ; I367N | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | benign  |
0.242 |
DELETERIOUS | 0.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1021960509 | NA | 5.58E-06 | mr1428_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 |
| vg1021960509 | NA | 1.27E-07 | mr1815_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 |