| Variant ID: vg1203842140 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 3842140 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
CACATGCATGCTGAATTAATTGAATTAACTCAATCCAAGCTTGAGCTAGGCATCTAGCTAACTTTGTGATTTGATCATGATCAGCTAGCAAAATCATCAT[A/C]
ATCATCATCATCATCATCTCCCTCTTCTCTTAATTTTTGAAAATTAATTAATTGACTGTGCTGATTGATAAGACCATCGTATTAACGTTAATTCGATCGA
TCGATCGAATTAACGTTAATACGATGGTCTTATCAATCAGCACAGTCAATTAATTAATTTTCAAAAATTAAGAGAAGAGGGAGATGATGATGATGATGAT[T/G]
ATGATGATTTTGCTAGCTGATCATGATCAAATCACAAAGTTAGCTAGATGCCTAGCTCAAGCTTGGATTGAGTTAATTCAATTAATTCAGCATGCATGTG
| Populations | Population Size | Frequency of A(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 34.60% | 6.70% | 18.68% | 40.06% | NA |
| All Indica | 2759 | 5.30% | 10.20% | 22.91% | 61.62% | NA |
| All Japonica | 1512 | 88.60% | 1.60% | 5.09% | 4.76% | NA |
| Aus | 269 | 8.90% | 0.40% | 56.51% | 34.20% | NA |
| Indica I | 595 | 4.40% | 0.80% | 44.37% | 50.42% | NA |
| Indica II | 465 | 6.00% | 3.90% | 16.99% | 73.12% | NA |
| Indica III | 913 | 4.10% | 16.80% | 15.44% | 63.75% | NA |
| Indica Intermediate | 786 | 6.90% | 13.50% | 18.83% | 60.81% | NA |
| Temperate Japonica | 767 | 97.10% | 1.70% | 0.65% | 0.52% | NA |
| Tropical Japonica | 504 | 76.20% | 1.00% | 11.51% | 11.31% | NA |
| Japonica Intermediate | 241 | 87.10% | 2.50% | 5.81% | 4.56% | NA |
| VI/Aromatic | 96 | 77.10% | 0.00% | 14.58% | 8.33% | NA |
| Intermediate | 90 | 58.90% | 8.90% | 8.89% | 23.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1203842140 | A -> C | LOC_Os12g07640.1 | 3_prime_UTR_variant ; 154.0bp to feature; MODIFIER | silent_mutation | Average:54.328; most accessible tissue: Zhenshan97 panicle, score: 83.904 | N | N | N | N |
| vg1203842140 | A -> DEL | N | N | silent_mutation | Average:54.328; most accessible tissue: Zhenshan97 panicle, score: 83.904 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1203842140 | NA | 2.37E-17 | mr1304 | 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 |
| vg1203842140 | NA | 1.76E-27 | mr1414 | 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 |
| vg1203842140 | NA | 9.21E-06 | mr1720 | 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 |
| vg1203842140 | 8.92E-07 | 8.92E-07 | mr1065_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 |
| vg1203842140 | NA | 5.60E-07 | mr1200_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 |
| vg1203842140 | 1.88E-06 | 1.88E-06 | mr1234_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 |
| vg1203842140 | NA | 2.04E-06 | mr1718_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 |