| Variant ID: vg1005564150 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 5564150 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.89, C: 0.11, others allele: 0.00, population size: 84. )
AATTGTTATTTGAACGGGCTGTAAGAGTGAATGATTGTTTGATTCCTCAAATTTTTTAATATAAATGTGTTGCACCAATTTTTGATGTGGAATATTTCTG[T/C]
TGTAGTAACCAAATAAATCAGTGTTACAATATTGCACAATTTGTTATGCTATCCTTTAAGCGTGTAGCGATGACCCATATTTTGTTGCGATATGGTTTAA
TTAAACCATATCGCAACAAAATATGGGTCATCGCTACACGCTTAAAGGATAGCATAACAAATTGTGCAATATTGTAACACTGATTTATTTGGTTACTACA[A/G]
CAGAAATATTCCACATCAAAAATTGGTGCAACACATTTATATTAAAAAATTTGAGGAATCAAACAATCATTCACTCTTACAGCCCGTTCAAATAACAATT
| 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 | 64.30% | 30.10% | 3.77% | 1.78% | NA |
| All Indica | 2759 | 42.80% | 49.40% | 4.89% | 2.86% | NA |
| All Japonica | 1512 | 95.90% | 1.90% | 1.92% | 0.26% | NA |
| Aus | 269 | 94.80% | 1.50% | 3.35% | 0.37% | NA |
| Indica I | 595 | 13.40% | 86.40% | 0.17% | 0.00% | NA |
| Indica II | 465 | 46.50% | 48.40% | 4.73% | 0.43% | NA |
| Indica III | 913 | 55.30% | 29.60% | 7.78% | 7.34% | NA |
| Indica Intermediate | 786 | 48.30% | 45.20% | 5.22% | 1.27% | NA |
| Temperate Japonica | 767 | 97.10% | 1.70% | 0.91% | 0.26% | NA |
| Tropical Japonica | 504 | 96.80% | 1.20% | 1.98% | 0.00% | NA |
| Japonica Intermediate | 241 | 90.00% | 4.10% | 4.98% | 0.83% | NA |
| VI/Aromatic | 96 | 91.70% | 7.30% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 73.30% | 22.20% | 4.44% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1005564150 | T -> C | LOC_Os10g10140.1 | downstream_gene_variant ; 254.0bp to feature; MODIFIER | silent_mutation | Average:22.128; most accessible tissue: Zhenshan97 flag leaf, score: 38.066 | N | N | N | N |
| vg1005564150 | T -> C | LOC_Os10g10149.1 | downstream_gene_variant ; 4674.0bp to feature; MODIFIER | silent_mutation | Average:22.128; most accessible tissue: Zhenshan97 flag leaf, score: 38.066 | N | N | N | N |
| vg1005564150 | T -> C | LOC_Os10g10140-LOC_Os10g10149 | intergenic_region ; MODIFIER | silent_mutation | Average:22.128; most accessible tissue: Zhenshan97 flag leaf, score: 38.066 | N | N | N | N |
| vg1005564150 | T -> DEL | N | N | silent_mutation | Average:22.128; most accessible tissue: Zhenshan97 flag leaf, score: 38.066 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1005564150 | NA | 6.69E-07 | mr1027_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 |
| vg1005564150 | 8.21E-07 | 8.21E-07 | mr1281_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 |
| vg1005564150 | NA | 3.65E-06 | mr1825_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 |
| vg1005564150 | NA | 8.18E-11 | mr1940_2 | 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 |
| vg1005564150 | 4.64E-06 | 4.64E-06 | mr1940_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 |