| Variant ID: vg0720611323 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 20611323 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.03, others allele: 0.00, population size: 109. )
ACCTGTTTTCTCGAGCTTACAAGTTGGCCATTCTTTTCTGACTAAGGCCTGGTTTCGTTCTTAACTTTTTTTAAAAAAAATTTTAACTTTTCTATCACAT[C/T]
AAAACTTTTCAACACACATAAACTTTAAACTTTTCCGTCACATCATTCTAATTTCAATCAAACTTTTAATTTTAGCGTGAAACTAAACACACCCTAAGAT
ATCTTAGGGTGTGTTTAGTTTCACGCTAAAATTAAAAGTTTGATTGAAATTAGAATGATGTGACGGAAAAGTTTAAAGTTTATGTGTGTTGAAAAGTTTT[G/A]
ATGTGATAGAAAAGTTAAAATTTTTTTTAAAAAAAGTTAAGAACGAAACCAGGCCTTAGTCAGAAAAGAATGGCCAACTTGTAAGCTCGAGAAAACAGGT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 83.70% | 13.40% | 2.88% | 0.00% | NA |
| All Indica | 2759 | 74.60% | 20.50% | 4.86% | 0.00% | NA |
| All Japonica | 1512 | 96.50% | 3.50% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 43.20% | 40.00% | 16.81% | 0.00% | NA |
| Indica II | 465 | 91.60% | 6.90% | 1.51% | 0.00% | NA |
| Indica III | 913 | 82.50% | 17.30% | 0.22% | 0.00% | NA |
| Indica Intermediate | 786 | 79.30% | 17.60% | 3.18% | 0.00% | NA |
| Temperate Japonica | 767 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 92.10% | 7.90% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 95.00% | 5.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 95.80% | 4.20% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 86.70% | 11.10% | 2.22% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0720611323 | C -> T | LOC_Os07g34390.1 | upstream_gene_variant ; 4391.0bp to feature; MODIFIER | silent_mutation | Average:41.643; most accessible tissue: Callus, score: 77.831 | N | N | N | N |
| vg0720611323 | C -> T | LOC_Os07g34380-LOC_Os07g34390 | intergenic_region ; MODIFIER | silent_mutation | Average:41.643; most accessible tissue: Callus, score: 77.831 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0720611323 | NA | 3.60E-06 | mr1200 | 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 |
| vg0720611323 | NA | 4.86E-08 | mr1215_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 |
| vg0720611323 | NA | 7.08E-09 | mr1220_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 |
| vg0720611323 | NA | 5.62E-06 | mr1220_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 |
| vg0720611323 | NA | 5.07E-06 | mr1422_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 |
| vg0720611323 | NA | 4.89E-07 | mr1629_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 |
| vg0720611323 | NA | 4.02E-06 | mr1835_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 |
| vg0720611323 | NA | 9.86E-06 | mr1863_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 |
| vg0720611323 | NA | 3.65E-08 | mr1904_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 |