Variant ID: vg1214134669 (JBrowse) | Variation Type: SNP |
Chromosome: chr12 | Position: 14134669 |
Reference Allele: G | Alternative Allele: A |
Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
AACAGATATTGTACGATACAATCGCGGAGGGAAGCAGCCAGTACTGGAATGAAGAAGAGGGAACGAGGATCCAAACCAGTACTTGAACGAGGAAGGGAAC[G/A]
TGGAGAGGGATGCGGAGGGAAACCAGTAGGGGCACGTGGAAAGGGATGTGGAGGGGAACCAGGAGGAGGAGGCTAGTGGTAGTCAACCCTCCGTTGGACA
TGTCCAACGGAGGGTTGACTACCACTAGCCTCCTCCTCCTGGTTCCCCTCCACATCCCTTTCCACGTGCCCCTACTGGTTTCCCTCCGCATCCCTCTCCA[C/T]
GTTCCCTTCCTCGTTCAAGTACTGGTTTGGATCCTCGTTCCCTCTTCTTCATTCCAGTACTGGCTGCTTCCCTCCGCGATTGTATCGTACAATATCTGTT
Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 18.70% | 0.20% | 2.03% | 79.09% | NA |
All Indica | 2759 | 4.70% | 0.40% | 2.46% | 92.46% | NA |
All Japonica | 1512 | 47.20% | 0.00% | 0.60% | 52.18% | NA |
Aus | 269 | 3.30% | 0.00% | 4.09% | 92.57% | NA |
Indica I | 595 | 2.20% | 0.20% | 1.85% | 95.80% | NA |
Indica II | 465 | 9.70% | 1.10% | 1.08% | 88.17% | NA |
Indica III | 913 | 3.00% | 0.10% | 2.96% | 93.98% | NA |
Indica Intermediate | 786 | 5.70% | 0.40% | 3.18% | 90.71% | NA |
Temperate Japonica | 767 | 76.90% | 0.00% | 0.26% | 22.82% | NA |
Tropical Japonica | 504 | 12.30% | 0.00% | 1.19% | 86.51% | NA |
Japonica Intermediate | 241 | 25.70% | 0.00% | 0.41% | 73.86% | NA |
VI/Aromatic | 96 | 2.10% | 0.00% | 3.12% | 94.79% | NA |
Intermediate | 90 | 30.00% | 0.00% | 5.56% | 64.44% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg1214134669 | G -> DEL | N | N | silent_mutation | Average:5.671; most accessible tissue: Minghui63 flower, score: 9.27 | N | N | N | N |
vg1214134669 | G -> A | LOC_Os12g24680.1 | intron_variant ; MODIFIER | silent_mutation | Average:5.671; most accessible tissue: Minghui63 flower, score: 9.27 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg1214134669 | NA | 2.33E-06 | mr1602 | 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 |
vg1214134669 | NA | 5.63E-06 | mr1606 | 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 |
vg1214134669 | 2.57E-07 | 2.57E-07 | mr1856 | 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 |
vg1214134669 | 3.30E-06 | 4.42E-06 | mr1881 | 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 |
vg1214134669 | NA | 3.36E-06 | mr1402_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 |
vg1214134669 | NA | 5.57E-06 | mr1795_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 |