Search for Variation information by Variation ID:
Detailed information for vg0417123204:
| Variant ID: vg0417123204 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 17123204 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 109. )
Flanking Sequence (100 bp) in Reference Genome:
CAGGAAATTATCTCACTACTTTCAAAGTCACCCGGTCACGGTAGTCATATCGTTTCCACTCGGGGATATACTTCATAACCGCGAAGCAAACGGACGGATC[G/A]
CGAAATGGGCCTTAGAATTGATGTCTTTGGAAGTATCGTTCAAGCCACGAACTTCGATCAAGTCACAAGCTTTAGCTGATTTCCTTGCCGAGTGGACCGA
Reverse complement sequence
TCGGTCCACTCGGCAAGGAAATCAGCTAAAGCTTGTGACTTGATCGAAGTTCGTGGCTTGAACGATACTTCCAAAGACATCAATTCTAAGGCCCATTTCG[C/T]
GATCCGTCCGTTTGCTTCGCGGTTATGAAGTATATCCCCGAGTGGAAACGATATGACTACCGTGACCGGGTGACTTTGAAAGTAGTGAGATAATTTCCTG
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 84.60% | 12.20% | 3.22% | 0.00% | NA |
| All Indica | 2759 | 95.80% | 1.90% | 2.28% | 0.00% | NA |
| All Japonica | 1512 | 67.10% | 27.70% | 5.16% | 0.00% | NA |
| Aus | 269 | 63.20% | 34.60% | 2.23% | 0.00% | NA |
| Indica I | 595 | 94.50% | 0.20% | 5.38% | 0.00% | NA |
| Indica II | 465 | 95.70% | 3.00% | 1.29% | 0.00% | NA |
| Indica III | 913 | 97.40% | 2.20% | 0.44% | 0.00% | NA |
| Indica Intermediate | 786 | 95.20% | 2.20% | 2.67% | 0.00% | NA |
| Temperate Japonica | 767 | 66.00% | 27.80% | 6.26% | 0.00% | NA |
| Tropical Japonica | 504 | 59.30% | 36.70% | 3.97% | 0.00% | NA |
| Japonica Intermediate | 241 | 87.10% | 8.70% | 4.15% | 0.00% | NA |
| VI/Aromatic | 96 | 97.90% | 1.00% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 82.20% | 13.30% | 4.44% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0417123204 | G -> A | LOC_Os04g28880.1 | missense_variant ; p.Ala1403Thr; MODERATE | nonsynonymous_codon ; A1403M | Average:33.312; most accessible tissue: Minghui63 young leaf, score: 55.178 | probably damaging  |
2.86 |
DELETERIOUS | 0.00 |
| vg0417123204 | G -> A | LOC_Os04g28880.1 | missense_variant ; p.Ala1403Thr; MODERATE | nonsynonymous_codon ; A1403T | Average:33.312; most accessible tissue: Minghui63 young leaf, score: 55.178 | benign |
0.73 |
TOLERATED | 0.05 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0417123204 | 2.07E-08 | NA | mr1301 | 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 |
| vg0417123204 | 9.91E-07 | NA | mr1410 | 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 |
| vg0417123204 | 6.02E-09 | NA | mr1301_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 |
| vg0417123204 | 6.95E-07 | NA | mr1301_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 |
| vg0417123204 | NA | 1.44E-06 | mr1363_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 |
| vg0417123204 | 4.02E-06 | NA | mr1410_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 |