| Variant ID: vg0401725881 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 1725881 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 232. )
TTTTGATCCTGCTAAACGTGTATGCATATATGGACATGGCCTTCATCCAGCTGGTATGTGATACCTCTCTTTTATTGACAAAATAAGTTTGCCATGAAAA[G/A]
TAGTGAAATGTAACTCCAAGTATATTCATCTGTGTTACAGGTCTTCTAATTGGACTTAGCTGTGGTATTGGAGTCCTTTTTCTTGTAGTAGGTCTAATTT
AAATTAGACCTACTACAAGAAAAAGGACTCCAATACCACAGCTAAGTCCAATTAGAAGACCTGTAACACAGATGAATATACTTGGAGTTACATTTCACTA[C/T]
TTTTCATGGCAAACTTATTTTGTCAATAAAAGAGAGGTATCACATACCAGCTGGATGAAGGCCATGTCCATATATGCATACACGTTTAGCAGGATCAAAA
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 58.70% | 5.30% | 1.44% | 34.55% | NA |
| All Indica | 2759 | 56.40% | 0.30% | 0.69% | 42.66% | NA |
| All Japonica | 1512 | 56.40% | 16.10% | 3.04% | 24.40% | NA |
| Aus | 269 | 90.30% | 0.00% | 0.00% | 9.67% | NA |
| Indica I | 595 | 22.20% | 0.00% | 0.50% | 77.31% | NA |
| Indica II | 465 | 77.40% | 0.40% | 1.08% | 21.08% | NA |
| Indica III | 913 | 70.40% | 0.10% | 0.33% | 29.13% | NA |
| Indica Intermediate | 786 | 53.60% | 0.50% | 1.02% | 44.91% | NA |
| Temperate Japonica | 767 | 70.70% | 2.00% | 1.83% | 25.55% | NA |
| Tropical Japonica | 504 | 36.90% | 35.50% | 4.56% | 23.02% | NA |
| Japonica Intermediate | 241 | 51.90% | 20.70% | 3.73% | 23.65% | NA |
| VI/Aromatic | 96 | 63.50% | 0.00% | 1.04% | 35.42% | NA |
| Intermediate | 90 | 66.70% | 1.10% | 2.22% | 30.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0401725881 | G -> DEL | N | N | silent_mutation | Average:30.027; most accessible tissue: Zhenshan97 young leaf, score: 63.096 | N | N | N | N |
| vg0401725881 | G -> A | LOC_Os04g03820.1 | downstream_gene_variant ; 4175.0bp to feature; MODIFIER | silent_mutation | Average:30.027; most accessible tissue: Zhenshan97 young leaf, score: 63.096 | N | N | N | N |
| vg0401725881 | G -> A | LOC_Os04g03830.1 | intron_variant ; MODIFIER | silent_mutation | Average:30.027; most accessible tissue: Zhenshan97 young leaf, score: 63.096 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0401725881 | NA | 9.06E-06 | mr1155 | 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 |
| vg0401725881 | NA | 2.67E-06 | mr1213 | 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 |
| vg0401725881 | 3.93E-07 | 8.23E-20 | mr1301 | 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 |
| vg0401725881 | NA | 5.87E-17 | mr1410 | 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 |
| vg0401725881 | 2.12E-07 | 3.35E-21 | mr1301_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 |
| vg0401725881 | NA | 2.08E-16 | mr1410_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 |
| vg0401725881 | 2.13E-08 | NA | mr1798_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 |
| vg0401725881 | NA | 1.10E-11 | mr1993_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 |