| Variant ID: vg0605702164 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 5702164 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
CTTTTCTAACTAAGATGCAGATTCTAACTTGATTTTTTTGTTCATATGTTTCATACAGAAACATTCTATATAGATATTGCCTTAAAATATTAAAAGTATC[T/C]
ACTTTTTAAATTTATATTAATTAAAACCATATTAATTATATGTTAATAATTTTCTCGTTTTACCATGAACGCTGTTGGAAAATTTCCATTTCCAACCGCT
AGCGGTTGGAAATGGAAATTTTCCAACAGCGTTCATGGTAAAACGAGAAAATTATTAACATATAATTAATATGGTTTTAATTAATATAAATTTAAAAAGT[A/G]
GATACTTTTAATATTTTAAGGCAATATCTATATAGAATGTTTCTGTATGAAACATATGAACAAAAAAATCAAGTTAGAATCTGCATCTTAGTTAGAAAAG
| 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 | 88.40% | 10.30% | 1.27% | 0.00% | NA |
| All Indica | 2759 | 97.80% | 2.00% | 0.22% | 0.00% | NA |
| All Japonica | 1512 | 78.60% | 18.10% | 3.31% | 0.00% | NA |
| Aus | 269 | 44.20% | 55.00% | 0.74% | 0.00% | NA |
| Indica I | 595 | 99.50% | 0.00% | 0.50% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 97.80% | 2.10% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 95.20% | 4.60% | 0.25% | 0.00% | NA |
| Temperate Japonica | 767 | 87.00% | 7.80% | 5.22% | 0.00% | NA |
| Tropical Japonica | 504 | 63.90% | 35.70% | 0.40% | 0.00% | NA |
| Japonica Intermediate | 241 | 83.00% | 13.70% | 3.32% | 0.00% | NA |
| VI/Aromatic | 96 | 96.90% | 2.10% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 88.90% | 10.00% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0605702164 | T -> C | LOC_Os06g10920.1 | downstream_gene_variant ; 2963.0bp to feature; MODIFIER | silent_mutation | Average:33.746; most accessible tissue: Callus, score: 52.93 | N | N | N | N |
| vg0605702164 | T -> C | LOC_Os06g10910.1 | intron_variant ; MODIFIER | silent_mutation | Average:33.746; most accessible tissue: Callus, score: 52.93 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0605702164 | 2.53E-07 | 9.13E-08 | mr1558_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 |
| vg0605702164 | NA | 1.43E-06 | mr1559_2 | 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 |
| vg0605702164 | NA | 5.68E-06 | mr1866_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 |