Search for Variation information by Variation ID:
Detailed information for vg1011510153:
| Variant ID: vg1011510153 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 11510153 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.64, G: 0.36, others allele: 0.00, population size: 59. )
Flanking Sequence (100 bp) in Reference Genome:
GTTCGGTCTCCCGAACTCGGCCGAGATCTACTCCAAGATCATCTCATCCGAGTTGGCTTCAAACCACTCGGACGAGATCTCATCTACTCCAACACGACCT[C/G]
ATCAAGATGATGGGGCCTATCCTTCAATCCTGATGAAGCTCCTCGATGATCTGGCTGCGGTCTTCACCACAAGGATGTCTTCTCCCCGTAGGTCTAGACG
Reverse complement sequence
CGTCTAGACCTACGGGGAGAAGACATCCTTGTGGTGAAGACCGCAGCCAGATCATCGAGGAGCTTCATCAGGATTGAAGGATAGGCCCCATCATCTTGAT[G/C]
AGGTCGTGTTGGAGTAGATGAGATCTCGTCCGAGTGGTTTGAAGCCAACTCGGATGAGATGATCTTGGAGTAGATCTCGGCCGAGTTCGGGAGACCGAAC
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 64.40% | 25.30% | 2.35% | 7.87% | NA |
| All Indica | 2759 | 86.20% | 13.40% | 0.40% | 0.00% | NA |
| All Japonica | 1512 | 19.20% | 50.30% | 6.08% | 24.40% | NA |
| Aus | 269 | 88.80% | 10.40% | 0.74% | 0.00% | NA |
| Indica I | 595 | 70.10% | 29.40% | 0.50% | 0.00% | NA |
| Indica II | 465 | 82.40% | 17.20% | 0.43% | 0.00% | NA |
| Indica III | 913 | 98.50% | 1.10% | 0.44% | 0.00% | NA |
| Indica Intermediate | 786 | 86.40% | 13.40% | 0.25% | 0.00% | NA |
| Temperate Japonica | 767 | 5.00% | 83.80% | 3.91% | 7.30% | NA |
| Tropical Japonica | 504 | 40.50% | 10.10% | 10.32% | 39.09% | NA |
| Japonica Intermediate | 241 | 19.90% | 27.80% | 4.15% | 48.13% | NA |
| VI/Aromatic | 96 | 84.40% | 15.60% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 63.30% | 26.70% | 6.67% | 3.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1011510153 | C -> G | LOC_Os10g22240.1 | missense_variant ; p.His85Asp; MODERATE | nonsynonymous_codon ; H85G | Average:44.147; most accessible tissue: Minghui63 flag leaf, score: 75.722 | benign  |
-1.322 |
DELETERIOUS | 0.01 |
| vg1011510153 | C -> G | LOC_Os10g22240.1 | missense_variant ; p.His85Asp; MODERATE | nonsynonymous_codon ; H85D | Average:44.147; most accessible tissue: Minghui63 flag leaf, score: 75.722 | probably damaging |
-3.052 |
TOLERATED | 1.00 |
| vg1011510153 | C -> DEL | LOC_Os10g22240.1 | N | frameshift_variant | Average:44.147; most accessible tissue: Minghui63 flag leaf, score: 75.722 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1011510153 | NA | 7.48E-06 | mr1277 | Jap_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 |
| vg1011510153 | NA | 1.82E-06 | mr1285 | 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 |
| vg1011510153 | NA | 4.70E-06 | mr1311 | 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 |
| vg1011510153 | NA | 1.28E-06 | mr1378 | 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 |
| vg1011510153 | NA | 6.87E-06 | mr1656 | 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 |
| vg1011510153 | NA | 2.75E-07 | mr1763 | 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 |
| vg1011510153 | NA | 3.87E-07 | mr1836 | 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 |
| vg1011510153 | NA | 9.54E-09 | mr1837 | 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 |