Variant ID: vg0603711280 (JBrowse) | Variation Type: SNP |
Chromosome: chr06 | Position: 3711280 |
Reference Allele: G | Alternative Allele: C |
Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
TAACATTATCGAAACTTTAGTTTGCCCTGAATCTGAGACAAAATTTCTGAACAAACAATAATCTTACCTTTCAACAATATAAGTGCCCGCGCATACGCGT[G/C]
GGCCACCTTACTAGTTTTACACTAAATTTTTGATACCTCATGGTATCTCCTCAAGGACCATAGAATTGCTCAAAGACTTCATGTCATGGAAAACTAAAGC
GCTTTAGTTTTCCATGACATGAAGTCTTTGAGCAATTCTATGGTCCTTGAGGAGATACCATGAGGTATCAAAAATTTAGTGTAAAACTAGTAAGGTGGCC[C/G]
ACGCGTATGCGCGGGCACTTATATTGTTGAAAGGTAAGATTATTGTTTGTTCAGAAATTTTGTCTCAGATTCAGGGCAAACTAAAGTTTCGATAATGTTA
Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 88.80% | 11.20% | 0.02% | 0.00% | NA |
All Indica | 2759 | 87.80% | 12.20% | 0.04% | 0.00% | NA |
All Japonica | 1512 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
Aus | 269 | 32.00% | 68.00% | 0.00% | 0.00% | NA |
Indica I | 595 | 77.50% | 22.40% | 0.17% | 0.00% | NA |
Indica II | 465 | 96.80% | 3.20% | 0.00% | 0.00% | NA |
Indica III | 913 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 77.40% | 22.60% | 0.00% | 0.00% | NA |
Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 97.90% | 2.10% | 0.00% | 0.00% | NA |
Intermediate | 90 | 95.60% | 4.40% | 0.00% | 0.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0603711280 | G -> C | LOC_Os06g07670.1 | upstream_gene_variant ; 2575.0bp to feature; MODIFIER | silent_mutation | Average:35.109; most accessible tissue: Zhenshan97 flag leaf, score: 49.845 | N | N | N | N |
vg0603711280 | G -> C | LOC_Os06g07660.1 | intron_variant ; MODIFIER | silent_mutation | Average:35.109; most accessible tissue: Zhenshan97 flag leaf, score: 49.845 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0603711280 | NA | 2.43E-08 | mr1184 | 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 |
vg0603711280 | NA | 6.93E-06 | mr1209 | 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 |
vg0603711280 | NA | 1.54E-07 | mr1629 | 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 |
vg0603711280 | NA | 1.19E-08 | mr1629_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 |