| Variant ID: vg1216589226 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 16589226 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
ACAAATCTTTTGAGCCTAATTAGTTAATAATTAGCCATAAGTGCTACAGTAACCCACATGTGCTAATGACAAATTAATTAGGCTTAAAAGATTCGTCTCG[T/C]
GGTTTTCAGGCGAGTTATGAAATTAGTTTTTTCCTTCGTGTCCGAAAACCCCTTCCGATATTCGGTCAAACGTCCGATGTGACAATCAAAAATTTTCTTT
AAAGAAAATTTTTGATTGTCACATCGGACGTTTGACCGAATATCGGAAGGGGTTTTCGGACACGAAGGAAAAAACTAATTTCATAACTCGCCTGAAAACC[A/G]
CGAGACGAATCTTTTAAGCCTAATTAATTTGTCATTAGCACATGTGGGTTACTGTAGCACTTATGGCTAATTATTAACTAATTAGGCTCAAAAGATTTGT
| 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 | 53.80% | 23.90% | 1.14% | 21.18% | NA |
| All Indica | 2759 | 65.90% | 7.50% | 1.52% | 25.08% | NA |
| All Japonica | 1512 | 24.80% | 57.50% | 0.53% | 17.20% | NA |
| Aus | 269 | 92.60% | 6.70% | 0.00% | 0.74% | NA |
| Indica I | 595 | 78.70% | 10.40% | 0.17% | 10.76% | NA |
| Indica II | 465 | 67.30% | 4.90% | 2.58% | 25.16% | NA |
| Indica III | 913 | 50.10% | 6.70% | 1.86% | 41.40% | NA |
| Indica Intermediate | 786 | 73.80% | 7.80% | 1.53% | 16.92% | NA |
| Temperate Japonica | 767 | 13.70% | 85.80% | 0.00% | 0.52% | NA |
| Tropical Japonica | 504 | 35.70% | 15.30% | 1.19% | 47.82% | NA |
| Japonica Intermediate | 241 | 37.30% | 55.60% | 0.83% | 6.22% | NA |
| VI/Aromatic | 96 | 66.70% | 8.30% | 1.04% | 23.96% | NA |
| Intermediate | 90 | 40.00% | 30.00% | 3.33% | 26.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1216589226 | T -> C | LOC_Os12g28100.1 | 3_prime_UTR_variant ; 1484.0bp to feature; MODIFIER | silent_mutation | Average:34.685; most accessible tissue: Callus, score: 57.876 | N | N | N | N |
| vg1216589226 | T -> C | LOC_Os12g28090.1 | downstream_gene_variant ; 3872.0bp to feature; MODIFIER | silent_mutation | Average:34.685; most accessible tissue: Callus, score: 57.876 | N | N | N | N |
| vg1216589226 | T -> DEL | N | N | silent_mutation | Average:34.685; most accessible tissue: Callus, score: 57.876 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1216589226 | NA | 3.57E-13 | mr1149 | 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 |
| vg1216589226 | 2.76E-06 | 2.76E-06 | mr1329 | 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 |
| vg1216589226 | NA | 9.10E-07 | mr1671 | 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 |
| vg1216589226 | NA | 1.85E-06 | mr1815 | 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 |
| vg1216589226 | NA | 7.56E-07 | mr1072_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 |
| vg1216589226 | NA | 5.08E-06 | mr1129_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 |
| vg1216589226 | NA | 5.11E-09 | mr1137_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 |
| vg1216589226 | 8.29E-06 | 8.29E-06 | mr1162_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 |
| vg1216589226 | NA | 4.12E-07 | mr1458_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 |
| vg1216589226 | NA | 1.78E-06 | mr1617_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 |