Search for Variation information by Variation ID:
Detailed information for vg1010531505:
| Variant ID: vg1010531505 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 10531505 |
| 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: 113. )
Flanking Sequence (100 bp) in Reference Genome:
TCCGGCCGCCTGGCGAGGAGGTACAGCATGTACTCCGACAGGGTCTCGCTGATGGACATCAAGCTCTGGATGTCGCCGTTCCGTGGCACTTCCATTTCGC[G/A]
GCGGCGGTGGGAGCACAGGTCCGTGGCGACGTGCCACAGCAGCAGGCACTCGTCGAACTCCCTTCTCACGCTTTCGCGCACGACGTCGTTCACGTTGAGC
Reverse complement sequence
GCTCAACGTGAACGACGTCGTGCGCGAAAGCGTGAGAAGGGAGTTCGACGAGTGCCTGCTGCTGTGGCACGTCGCCACGGACCTGTGCTCCCACCGCCGC[C/T]
GCGAAATGGAAGTGCCACGGAACGGCGACATCCAGAGCTTGATGTCCATCAGCGAGACCCTGTCGGAGTACATGCTGTACCTCCTCGCCAGGCGGCCGGA
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 | 90.30% | 9.60% | 0.15% | 0.00% | NA |
| All Indica | 2759 | 83.70% | 16.10% | 0.25% | 0.00% | NA |
| All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 98.50% | 1.30% | 0.17% | 0.00% | NA |
| Indica II | 465 | 88.80% | 10.80% | 0.43% | 0.00% | NA |
| Indica III | 913 | 72.20% | 27.40% | 0.44% | 0.00% | NA |
| Indica Intermediate | 786 | 82.70% | 17.30% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 92.20% | 7.80% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1010531505 | G -> A | LOC_Os10g20770.1 | missense_variant ; p.Arg543Cys; MODERATE | nonsynonymous_codon ; R543C | Average:75.456; most accessible tissue: Zhenshan97 young leaf, score: 83.199 | benign  |
0.467 |
TOLERATED | 0.06 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1010531505 | NA | 2.81E-11 | mr1118 | 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 |
| vg1010531505 | 3.08E-07 | NA | mr1258_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 |
| vg1010531505 | 4.60E-06 | 5.06E-07 | mr1258_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 |