| Variant ID: vg1001790923 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 1790923 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.91, T: 0.09, others allele: 0.00, population size: 113. )
CTAATAGACCCATCGCCCAATCAACGGCTCAGATCGTGTTTCAGTCGATAAAAACAGTACTACCTCCGTTTCATAATGTAAGTCATTCTAGCATTGCCCA[C/T]
ATTCATATAGATACTAATGAATCTAAACATATATGTGTGTCTAGATTTATTAACATCTATATGAATGTGGATAATACTAGAAAGTCTTACATTATGAAAC
GTTTCATAATGTAAGACTTTCTAGTATTATCCACATTCATATAGATGTTAATAAATCTAGACACACATATATGTTTAGATTCATTAGTATCTATATGAAT[G/A]
TGGGCAATGCTAGAATGACTTACATTATGAAACGGAGGTAGTACTGTTTTTATCGACTGAAACACGATCTGAGCCGTTGATTGGGCGATGGGTCTATTAG
| 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 | 51.60% | 17.80% | 0.42% | 30.13% | NA |
| All Indica | 2759 | 29.80% | 19.30% | 0.69% | 50.24% | NA |
| All Japonica | 1512 | 94.40% | 4.00% | 0.07% | 1.52% | NA |
| Aus | 269 | 12.60% | 87.00% | 0.00% | 0.37% | NA |
| Indica I | 595 | 46.70% | 3.00% | 0.34% | 49.92% | NA |
| Indica II | 465 | 23.40% | 14.40% | 1.72% | 60.43% | NA |
| Indica III | 913 | 22.10% | 32.20% | 0.33% | 45.35% | NA |
| Indica Intermediate | 786 | 29.50% | 19.60% | 0.76% | 50.13% | NA |
| Temperate Japonica | 767 | 99.20% | 0.10% | 0.13% | 0.52% | NA |
| Tropical Japonica | 504 | 85.10% | 11.50% | 0.00% | 3.37% | NA |
| Japonica Intermediate | 241 | 98.80% | 0.40% | 0.00% | 0.83% | NA |
| VI/Aromatic | 96 | 95.80% | 4.20% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 71.10% | 13.30% | 0.00% | 15.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1001790923 | C -> T | LOC_Os10g03930.1 | upstream_gene_variant ; 2844.0bp to feature; MODIFIER | silent_mutation | Average:47.825; most accessible tissue: Zhenshan97 root, score: 81.974 | N | N | N | N |
| vg1001790923 | C -> T | LOC_Os10g03950.1 | upstream_gene_variant ; 1292.0bp to feature; MODIFIER | silent_mutation | Average:47.825; most accessible tissue: Zhenshan97 root, score: 81.974 | N | N | N | N |
| vg1001790923 | C -> T | LOC_Os10g03930-LOC_Os10g03950 | intergenic_region ; MODIFIER | silent_mutation | Average:47.825; most accessible tissue: Zhenshan97 root, score: 81.974 | N | N | N | N |
| vg1001790923 | C -> DEL | N | N | silent_mutation | Average:47.825; most accessible tissue: Zhenshan97 root, score: 81.974 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1001790923 | 2.70E-07 | NA | mr1486 | 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 |
| vg1001790923 | 4.48E-07 | NA | mr1548 | 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 |
| vg1001790923 | 3.63E-09 | NA | mr1486_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 |
| vg1001790923 | 5.52E-10 | 1.85E-06 | mr1588_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 |