Variant ID: vg1122375960 (JBrowse) | Variation Type: SNP |
Chromosome: chr11 | Position: 22375960 |
Reference Allele: T | Alternative Allele: C |
Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GTCATTTCCATTGGAAATGGGGAGAAAATAAAATTCTTGACAGATAATTGGTTGCAGGGGAGCTCTCCCAAAGAAATAACGCCTTCAATCTTCCGACTAG[T/C]
GAAGAGGAAATCAAACTGTCTAAAATGGGATTTTGAGAGCAATCACTGGATGGCATGGAAGTGTCTAAAAGAACTTTTACGGTACAATATACTAACAATA
TATTGTTAGTATATTGTACCGTAAAAGTTCTTTTAGACACTTCCATGCCATCCAGTGATTGCTCTCAAAATCCCATTTTAGACAGTTTGATTTCCTCTTC[A/G]
CTAGTCGGAAGATTGAAGGCGTTATTTCTTTGGGAGAGCTCCCCTGCAACCAATTATCTGTCAAGAATTTTATTTTCTCCCCATTTCCAATGGAAATGAC
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 | 65.80% | 24.70% | 2.03% | 7.43% | NA |
All Indica | 2759 | 79.20% | 16.20% | 1.85% | 2.72% | NA |
All Japonica | 1512 | 36.20% | 43.40% | 2.58% | 17.79% | NA |
Aus | 269 | 82.50% | 15.60% | 1.86% | 0.00% | NA |
Indica I | 595 | 57.00% | 35.00% | 4.37% | 3.70% | NA |
Indica II | 465 | 76.30% | 19.60% | 2.80% | 1.29% | NA |
Indica III | 913 | 96.10% | 0.90% | 0.44% | 2.63% | NA |
Indica Intermediate | 786 | 78.20% | 17.80% | 1.02% | 2.93% | NA |
Temperate Japonica | 767 | 21.90% | 69.40% | 2.22% | 6.52% | NA |
Tropical Japonica | 504 | 50.80% | 15.10% | 2.58% | 31.55% | NA |
Japonica Intermediate | 241 | 51.50% | 19.90% | 3.73% | 24.90% | NA |
VI/Aromatic | 96 | 97.90% | 2.10% | 0.00% | 0.00% | NA |
Intermediate | 90 | 66.70% | 24.40% | 1.11% | 7.78% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg1122375960 | T -> DEL | N | N | silent_mutation | Average:24.047; most accessible tissue: Callus, score: 66.8 | N | N | N | N |
vg1122375960 | T -> C | LOC_Os11g37780-LOC_Os11g37790 | intergenic_region ; MODIFIER | silent_mutation | Average:24.047; most accessible tissue: Callus, score: 66.8 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg1122375960 | NA | 5.06E-07 | mr1045 | 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 |
vg1122375960 | 1.12E-06 | 1.12E-06 | mr1060 | 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 |
vg1122375960 | NA | 2.70E-06 | mr1126 | 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 |
vg1122375960 | NA | 4.97E-06 | mr1147 | 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 |
vg1122375960 | NA | 5.07E-06 | mr1156 | 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 |
vg1122375960 | NA | 8.06E-06 | mr1164 | 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 |
vg1122375960 | NA | 5.41E-06 | mr1179 | 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 |
vg1122375960 | NA | 8.10E-06 | mr1359 | 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 |
vg1122375960 | NA | 2.78E-06 | mr1380 | 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 |
vg1122375960 | NA | 3.52E-06 | mr1502 | 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 |
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