| Variant ID: vg0209234214 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 9234214 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CTGATTGCAATTTAAAATTACCATTTCATTGAACTCAGGGGAGAGTTCTTTTCCATTCCAATGCTGTATGAATTTCAATGTGTGCAAGCCACATGACCAG[C/T]
TGTTGCAAGCATGTCCTTTGTTAGTGGTAATTCGTTATAGATAATTTGCGACAAAAATTAACTGTTTGTTTGACCTGTCACTTTGCTGAGGGACTTTCAT
ATGAAAGTCCCTCAGCAAAGTGACAGGTCAAACAAACAGTTAATTTTTGTCGCAAATTATCTATAACGAATTACCACTAACAAAGGACATGCTTGCAACA[G/A]
CTGGTCATGTGGCTTGCACACATTGAAATTCATACAGCATTGGAATGGAAAAGAACTCTCCCCTGAGTTCAATGAAATGGTAATTTTAAATTGCAATCAG
| 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 | 79.90% | 8.00% | 3.28% | 8.84% | NA |
| All Indica | 2759 | 67.90% | 13.20% | 5.04% | 13.92% | NA |
| All Japonica | 1512 | 98.50% | 0.00% | 0.07% | 1.46% | NA |
| Aus | 269 | 90.30% | 4.50% | 5.20% | 0.00% | NA |
| Indica I | 595 | 61.30% | 13.10% | 1.34% | 24.20% | NA |
| Indica II | 465 | 78.90% | 4.50% | 2.80% | 13.76% | NA |
| Indica III | 913 | 61.00% | 22.60% | 9.53% | 6.90% | NA |
| Indica Intermediate | 786 | 74.20% | 7.50% | 3.94% | 14.38% | NA |
| Temperate Japonica | 767 | 98.70% | 0.00% | 0.00% | 1.30% | NA |
| Tropical Japonica | 504 | 98.20% | 0.00% | 0.20% | 1.59% | NA |
| Japonica Intermediate | 241 | 98.30% | 0.00% | 0.00% | 1.66% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 85.60% | 0.00% | 1.11% | 13.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0209234214 | C -> T | LOC_Os02g16240.1 | splice_acceptor_variant&intron_variant ; HIGH | splice_acceptor_variant | Average:7.25; most accessible tissue: Callus, score: 24.364 | N | N | N | N |
| vg0209234214 | C -> DEL | LOC_Os02g16240.1 | N | splice_acceptor_variant | Average:7.25; most accessible tissue: Callus, score: 24.364 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0209234214 | NA | 6.57E-06 | mr1795 | 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 |
| vg0209234214 | 1.71E-06 | NA | mr1861 | 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 |
| vg0209234214 | 4.70E-06 | NA | mr1861 | 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 |