| Variant ID: vg0223422221 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 23422221 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 47. )
AAAGATTTCCTTGTCAAGGGGAAGGTGCAAGCAGTCCCGAAACGAAGAACTCATACCGCGGTTGTGGCTTTCCTTTGGAGCCGCTCAAATGTCTTCTGCG[T/C]
ATGAAGAAATAGGAGTGCACTACATAGAGGATCCAACTTACCTTTTATGCCAACTCGATGAGTGTTTTTTTAGTTAACTCATTCATTCAAAATATGCACT
AGTGCATATTTTGAATGAATGAGTTAACTAAAAAAACACTCATCGAGTTGGCATAAAAGGTAAGTTGGATCCTCTATGTAGTGCACTCCTATTTCTTCAT[A/G]
CGCAGAAGACATTTGAGCGGCTCCAAAGGAAAGCCACAACCGCGGTATGAGTTCTTCGTTTCGGGACTGCTTGCACCTTCCCCTTGACAAGGAAATCTTT
| 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 | 31.60% | 28.70% | 1.33% | 38.38% | NA |
| All Indica | 2759 | 51.40% | 6.40% | 1.63% | 40.56% | NA |
| All Japonica | 1512 | 3.00% | 73.10% | 0.93% | 23.02% | NA |
| Aus | 269 | 1.90% | 5.60% | 1.12% | 91.45% | NA |
| Indica I | 595 | 62.50% | 8.70% | 0.84% | 27.90% | NA |
| Indica II | 465 | 61.90% | 7.30% | 3.44% | 27.31% | NA |
| Indica III | 913 | 35.30% | 2.20% | 1.20% | 61.34% | NA |
| Indica Intermediate | 786 | 55.50% | 9.00% | 1.65% | 33.84% | NA |
| Temperate Japonica | 767 | 2.20% | 81.60% | 0.78% | 15.38% | NA |
| Tropical Japonica | 504 | 5.40% | 59.30% | 0.99% | 34.33% | NA |
| Japonica Intermediate | 241 | 0.40% | 74.70% | 1.24% | 23.65% | NA |
| VI/Aromatic | 96 | 11.50% | 14.60% | 1.04% | 72.92% | NA |
| Intermediate | 90 | 16.70% | 48.90% | 0.00% | 34.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0223422221 | T -> DEL | N | N | silent_mutation | Average:55.776; most accessible tissue: Minghui63 flag leaf, score: 79.676 | N | N | N | N |
| vg0223422221 | T -> C | LOC_Os02g38750.1 | upstream_gene_variant ; 3465.0bp to feature; MODIFIER | silent_mutation | Average:55.776; most accessible tissue: Minghui63 flag leaf, score: 79.676 | N | N | N | N |
| vg0223422221 | T -> C | LOC_Os02g38770.1 | upstream_gene_variant ; 4425.0bp to feature; MODIFIER | silent_mutation | Average:55.776; most accessible tissue: Minghui63 flag leaf, score: 79.676 | N | N | N | N |
| vg0223422221 | T -> C | LOC_Os02g38760.1 | intron_variant ; MODIFIER | silent_mutation | Average:55.776; most accessible tissue: Minghui63 flag leaf, score: 79.676 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0223422221 | NA | 6.91E-06 | mr1148_2 | Jap_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 |
| vg0223422221 | 6.77E-06 | 6.77E-06 | mr1279_2 | Jap_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 |
| vg0223422221 | 8.65E-06 | 8.65E-06 | mr1372_2 | Jap_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 |
| vg0223422221 | 5.44E-07 | 5.44E-07 | mr1440_2 | Jap_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 |
| vg0223422221 | NA | 1.55E-06 | mr1896_2 | Jap_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 |