Search for Variation information by Variation ID:
Detailed information for vg1010550381:
| Variant ID: vg1010550381 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 10550381 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TTCCTGGCGAGGGGACCATCTGGCTCGATCGCGACATTCCAGGGATATGAAATCAATGGGTACACATTCTACACGAGAGCCCAAGACATGAAGAGCACGA[G/A]
CCAGAACAGTGTTGTTCGTATCGATGCCATGGGACACGATGGTACAACTAGCACGTATTACGGTGCCATCGAGGACATATGGGAACTTGACTATGGACCT
Reverse complement sequence
AGGTCCATAGTCAAGTTCCCATATGTCCTCGATGGCACCGTAATACGTGCTAGTTGTACCATCGTGTCCCATGGCATCGATACGAACAACACTGTTCTGG[C/T]
TCGTGCTCTTCATGTCTTGGGCTCTCGTGTAGAATGTGTACCCATTGATTTCATATCCCTGGAATGTCGCGATCGAGCCAGATGGTCCCCTCGCCAGGAA
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 63.40% | 28.10% | 8.46% | 0.00% | NA |
| All Indica | 2759 | 89.60% | 5.00% | 5.36% | 0.00% | NA |
| All Japonica | 1512 | 11.60% | 74.30% | 14.09% | 0.00% | NA |
| Aus | 269 | 85.10% | 4.50% | 10.41% | 0.00% | NA |
| Indica I | 595 | 89.40% | 5.20% | 5.38% | 0.00% | NA |
| Indica II | 465 | 84.10% | 6.20% | 9.68% | 0.00% | NA |
| Indica III | 913 | 91.90% | 4.80% | 3.29% | 0.00% | NA |
| Indica Intermediate | 786 | 90.50% | 4.30% | 5.22% | 0.00% | NA |
| Temperate Japonica | 767 | 3.00% | 85.30% | 11.73% | 0.00% | NA |
| Tropical Japonica | 504 | 24.60% | 59.50% | 15.87% | 0.00% | NA |
| Japonica Intermediate | 241 | 11.60% | 70.50% | 17.84% | 0.00% | NA |
| VI/Aromatic | 96 | 76.00% | 21.90% | 2.08% | 0.00% | NA |
| Intermediate | 90 | 52.20% | 37.80% | 10.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1010550381 | G -> A | LOC_Os10g20794.1 | missense_variant ; p.Ser624Asn; MODERATE | nonsynonymous_codon ; S624N | Average:18.105; most accessible tissue: Minghui63 panicle, score: 38.588 | benign  |
-1.021 |
TOLERATED | 1.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1010550381 | NA | 4.60E-07 | mr1690 | 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 |
| vg1010550381 | 1.47E-06 | 1.72E-07 | mr1768 | 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 |
| vg1010550381 | NA | 9.75E-09 | mr1576_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 |