| Variant ID: vg0204625031 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 4625031 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GGTATTGTTTAGTTGGGAAAAAAATTTGGGGTTGGTTGTCACATCAGATATACGGATACACATTTGAAGTAATAAAGTAATAATAAAACAAATTTCACTA[G/T]
AAAACCGCGAAATGAATTTATTAAACCTAATTAATCATCATTAGCAAATGTTTACTGTAGCATCACATTGTCAAATCATGGTGCAATTAGTCTTATAAGA
TCTTATAAGACTAATTGCACCATGATTTGACAATGTGATGCTACAGTAAACATTTGCTAATGATGATTAATTAGGTTTAATAAATTCATTTCGCGGTTTT[C/A]
TAGTGAAATTTGTTTTATTATTACTTTATTACTTCAAATGTGTATCCGTATATCTGATGTGACAACCAACCCCAAATTTTTTTCCCAACTAAACAATACC
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 96.10% | 3.90% | 0.04% | 0.00% | NA |
| All Indica | 2759 | 93.50% | 6.50% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 96.80% | 3.20% | 0.00% | 0.00% | NA |
| Indica III | 913 | 88.80% | 11.20% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 92.10% | 7.90% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 93.30% | 4.40% | 2.22% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0204625031 | G -> T | LOC_Os02g08544.1 | upstream_gene_variant ; 364.0bp to feature; MODIFIER | silent_mutation | Average:69.109; most accessible tissue: Minghui63 panicle, score: 87.951 | N | N | N | N |
| vg0204625031 | G -> T | LOC_Os02g08544.2 | upstream_gene_variant ; 364.0bp to feature; MODIFIER | silent_mutation | Average:69.109; most accessible tissue: Minghui63 panicle, score: 87.951 | N | N | N | N |
| vg0204625031 | G -> T | LOC_Os02g08544.3 | upstream_gene_variant ; 1753.0bp to feature; MODIFIER | silent_mutation | Average:69.109; most accessible tissue: Minghui63 panicle, score: 87.951 | N | N | N | N |
| vg0204625031 | G -> T | LOC_Os02g08540.1 | downstream_gene_variant ; 2920.0bp to feature; MODIFIER | silent_mutation | Average:69.109; most accessible tissue: Minghui63 panicle, score: 87.951 | N | N | N | N |
| vg0204625031 | G -> T | LOC_Os02g09050.1 | downstream_gene_variant ; 4563.0bp to feature; MODIFIER | silent_mutation | Average:69.109; most accessible tissue: Minghui63 panicle, score: 87.951 | N | N | N | N |
| vg0204625031 | G -> T | LOC_Os02g08540-LOC_Os02g08544 | intergenic_region ; MODIFIER | silent_mutation | Average:69.109; most accessible tissue: Minghui63 panicle, score: 87.951 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0204625031 | 4.32E-06 | 1.91E-06 | mr1120_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 |
| vg0204625031 | 9.75E-06 | NA | mr1123_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 |
| vg0204625031 | 4.35E-06 | 6.52E-06 | mr1247_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 |
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