| Variant ID: vg0909731506 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 9731506 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
ATAAATGTAAGGGAGTACAAGGGGGTTATAATATAAGGGTTAGGGTTTGCAGTAAACAGCATTAAAAGACACTTAGTTGCTCAAAGCTATTTTGTGAACA[T/C]
GGTCCTAGAGCTATACAATATTATTAACCAAGGCCGTAAACCCACACGAACCTGCCTTAACCCAAGGCCTACGATGATTCAGACCGAACTGGCAACCCGA
TCGGGTTGCCAGTTCGGTCTGAATCATCGTAGGCCTTGGGTTAAGGCAGGTTCGTGTGGGTTTACGGCCTTGGTTAATAATATTGTATAGCTCTAGGACC[A/G]
TGTTCACAAAATAGCTTTGAGCAACTAAGTGTCTTTTAATGCTGTTTACTGCAAACCCTAACCCTTATATTATAACCCCCTTGTACTCCCTTACATTTAT
| 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 | 24.00% | 9.80% | 6.94% | 59.25% | NA |
| All Indica | 2759 | 15.40% | 0.60% | 8.52% | 75.50% | NA |
| All Japonica | 1512 | 43.50% | 28.40% | 3.90% | 24.21% | NA |
| Aus | 269 | 1.50% | 1.50% | 6.32% | 90.71% | NA |
| Indica I | 595 | 1.70% | 0.80% | 7.90% | 89.58% | NA |
| Indica II | 465 | 2.40% | 0.60% | 9.25% | 87.74% | NA |
| Indica III | 913 | 31.90% | 0.10% | 8.11% | 59.91% | NA |
| Indica Intermediate | 786 | 14.20% | 1.00% | 9.03% | 75.70% | NA |
| Temperate Japonica | 767 | 28.60% | 48.90% | 4.82% | 17.73% | NA |
| Tropical Japonica | 504 | 61.30% | 2.60% | 2.78% | 33.33% | NA |
| Japonica Intermediate | 241 | 53.50% | 17.40% | 3.32% | 25.73% | NA |
| VI/Aromatic | 96 | 22.90% | 2.10% | 7.29% | 67.71% | NA |
| Intermediate | 90 | 28.90% | 13.30% | 11.11% | 46.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0909731506 | T -> DEL | N | N | silent_mutation | Average:7.391; most accessible tissue: Zhenshan97 flower, score: 15.748 | N | N | N | N |
| vg0909731506 | T -> C | LOC_Os09g15930-LOC_Os09g15940 | intergenic_region ; MODIFIER | silent_mutation | Average:7.391; most accessible tissue: Zhenshan97 flower, score: 15.748 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0909731506 | 3.78E-06 | NA | mr1108 | 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 |
| vg0909731506 | NA | 2.47E-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 |
| vg0909731506 | NA | 1.27E-07 | mr1078_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 |