Search for Variation information by Variation ID:
Detailed information for vg1000328907:
| Variant ID: vg1000328907 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 328907 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, G: 0.02, others allele: 0.00, population size: 286. )
Flanking Sequence (100 bp) in Reference Genome:
GGAGTTCTTGCAATGGAAGGCAAAAAATGGGGTTAGTGACAAGGCATTTGGCGATTTATTGAAACTCGTCAAGAACATTCTTCCGGAGGGAAACAAATTG[C/G]
CCGAGTACGAGGCTAAGAAGATAGTCTGCCCGCTAGGACTGGAAGTTCAGAAGATTCACGCATGTCCGAATGATTGTATCCTATATCGCGGTGAGTATGA
Reverse complement sequence
TCATACTCACCGCGATATAGGATACAATCATTCGGACATGCGTGAATCTTCTGAACTTCCAGTCCTAGCGGGCAGACTATCTTCTTAGCCTCGTACTCGG[G/C]
CAATTTGTTTCCCTCCGGAAGAATGTTCTTGACGAGTTTCAATAAATCGCCAAATGCCTTGTCACTAACCCCATTTTTTGCCTTCCATTGCAAGAACTCC
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 67.60% | 32.10% | 0.25% | 0.00% | NA |
| All Indica | 2759 | 49.30% | 50.30% | 0.36% | 0.00% | NA |
| All Japonica | 1512 | 98.50% | 1.50% | 0.00% | 0.00% | NA |
| Aus | 269 | 66.20% | 33.80% | 0.00% | 0.00% | NA |
| Indica I | 595 | 41.50% | 58.20% | 0.34% | 0.00% | NA |
| Indica II | 465 | 48.20% | 51.80% | 0.00% | 0.00% | NA |
| Indica III | 913 | 60.10% | 39.50% | 0.33% | 0.00% | NA |
| Indica Intermediate | 786 | 43.30% | 56.10% | 0.64% | 0.00% | NA |
| Temperate Japonica | 767 | 99.10% | 0.90% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 97.80% | 2.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.30% | 1.70% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 78.90% | 18.90% | 2.22% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1000328907 | C -> G | LOC_Os10g01510.1 | missense_variant ; p.Pro200Ala; MODERATE | nonsynonymous_codon ; P200A | Average:14.807; most accessible tissue: Zhenshan97 root, score: 22.162 | possibly damaging  |
1.82 |
DELETERIOUS | 0.01 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1000328907 | 9.22E-06 | NA | mr1383 | 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 |
| vg1000328907 | NA | 5.07E-07 | mr1383 | 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 |
| vg1000328907 | NA | 1.14E-12 | mr1449 | 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 |
| vg1000328907 | 9.22E-07 | 9.22E-07 | mr1449 | 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 |
| vg1000328907 | NA | 5.43E-07 | mr1168_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 |
| vg1000328907 | 4.61E-07 | NA | mr1383_2 | 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 |