| Variant ID: vg0333155926 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 33155926 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 116. )
TGGAGTTCACCACCTTCGGAGTGAAGGAAGAACTACCCCGAGTGATTGAGGCTTGGGTAGTCCTCTCCGTGGGCCGGCTCCCGCCTTGCCCACCCCTTGA[C/T]
GAAGGGAGCGTGTGGTGGCTTCGTGGTTGAGCGGTGGAGTTGGGCTCGCCTCAACGGGGATTAGGAAACCGGCGAGTTTCTGAACCTCGGTGAAAAATTC
GAATTTTTCACCGAGGTTCAGAAACTCGCCGGTTTCCTAATCCCCGTTGAGGCGAGCCCAACTCCACCGCTCAACCACGAAGCCACCACACGCTCCCTTC[G/A]
TCAAGGGGTGGGCAAGGCGGGAGCCGGCCCACGGAGAGGACTACCCAAGCCTCAATCACTCGGGGTAGTTCTTCCTTCACTCCGAAGGTGGTGAACTCCA
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 52.00% | 40.90% | 6.35% | 0.78% | NA |
| All Indica | 2759 | 78.30% | 9.80% | 10.62% | 1.34% | NA |
| All Japonica | 1512 | 0.70% | 99.20% | 0.13% | 0.00% | NA |
| Aus | 269 | 94.40% | 5.60% | 0.00% | 0.00% | NA |
| Indica I | 595 | 72.60% | 10.30% | 16.81% | 0.34% | NA |
| Indica II | 465 | 75.70% | 8.20% | 15.91% | 0.22% | NA |
| Indica III | 913 | 85.90% | 5.30% | 5.70% | 3.18% | NA |
| Indica Intermediate | 786 | 75.20% | 15.60% | 8.52% | 0.64% | NA |
| Temperate Japonica | 767 | 0.50% | 99.50% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 1.20% | 98.60% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 0.00% | 99.60% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 1.00% | 99.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 35.60% | 58.90% | 5.56% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0333155926 | C -> T | LOC_Os03g58220.1 | intron_variant ; MODIFIER | silent_mutation | Average:30.617; most accessible tissue: Minghui63 panicle, score: 59.629 | N | N | N | N |
| vg0333155926 | C -> DEL | N | N | silent_mutation | Average:30.617; most accessible tissue: Minghui63 panicle, score: 59.629 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0333155926 | NA | 3.27E-34 | mr1723 | 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 |
| vg0333155926 | 4.42E-08 | 5.45E-42 | mr1723_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 |
| vg0333155926 | 1.95E-06 | 1.35E-08 | mr1723_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 |