Search for Variation information by Variation ID:
Detailed information for vg1000646061:
| Variant ID: vg1000646061 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 646061 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.83, A: 0.17, others allele: 0.00, population size: 54. )
Flanking Sequence (100 bp) in Reference Genome:
AACTTGCGTTACATCATTGGCAAGGACAAAAGGTTCGTCCGAGTATCCAACCTTGTTAAGGTCAACCGTTGTGATCCCACTGTCATCAATCGTTACGCCT[A/C]
CACCAGTCAACCTAACCCATTGCCACCGAAACAGAGGGACCTTGAGAGGTCCATAGTCAAGTTCCCATATCTCCTCGATGGCACCGTAATACGTGCTAGT
Reverse complement sequence
ACTAGCACGTATTACGGTGCCATCGAGGAGATATGGGAACTTGACTATGGACCTCTCAAGGTCCCTCTGTTTCGGTGGCAATGGGTTAGGTTGACTGGTG[T/G]
AGGCGTAACGATTGATGACAGTGGGATCACAACGGTTGACCTTAACAAGGTTGGATACTCGGACGAACCTTTTGTCCTTGCCAATGATGTAACGCAAGTT
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 17.70% | 1.40% | 16.14% | 64.81% | NA |
| All Indica | 2759 | 1.60% | 0.10% | 21.17% | 77.20% | NA |
| All Japonica | 1512 | 49.90% | 4.10% | 0.99% | 45.04% | NA |
| Aus | 269 | 3.00% | 0.00% | 35.69% | 61.34% | NA |
| Indica I | 595 | 2.40% | 0.00% | 26.89% | 70.76% | NA |
| Indica II | 465 | 1.90% | 0.00% | 4.30% | 93.76% | NA |
| Indica III | 913 | 0.80% | 0.00% | 28.37% | 70.87% | NA |
| Indica Intermediate | 786 | 1.70% | 0.30% | 18.45% | 79.64% | NA |
| Temperate Japonica | 767 | 79.90% | 7.30% | 0.13% | 12.65% | NA |
| Tropical Japonica | 504 | 6.30% | 0.00% | 1.59% | 92.06% | NA |
| Japonica Intermediate | 241 | 45.20% | 2.50% | 2.49% | 49.79% | NA |
| VI/Aromatic | 96 | 9.40% | 0.00% | 59.38% | 31.25% | NA |
| Intermediate | 90 | 23.30% | 1.10% | 12.22% | 63.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1000646061 | A -> C | LOC_Os10g02030.1 | missense_variant ; p.Val747Gly; MODERATE | nonsynonymous_codon ; V747G | Average:5.786; most accessible tissue: Callus, score: 10.549 | probably damaging  |
-2.308 |
TOLERATED | 1.00 |
| vg1000646061 | A -> DEL | LOC_Os10g02030.1 | N | frameshift_variant | Average:5.786; most accessible tissue: Callus, score: 10.549 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1000646061 | NA | 2.06E-09 | mr1757 | 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 |
| vg1000646061 | 6.88E-09 | NA | mr1310_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 |
| vg1000646061 | 1.46E-09 | NA | mr1310_2 | 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 |
| vg1000646061 | NA | 7.60E-06 | mr1354_2 | 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 |
| vg1000646061 | NA | 1.23E-08 | mr1549_2 | 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 |
| vg1000646061 | NA | 7.14E-07 | mr1757_2 | 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 |