Variant ID: vg1217642122 (JBrowse) | Variation Type: INDEL |
Chromosome: chr12 | Position: 17642122 |
Reference Allele: AAGCTACATTTACAGTTAACTGG | Alternative Allele: TAGCTACATTTACAGTTAACTGG,A |
Primary Allele: AAGCTACATTTACAGTTAAC TGG | Secondary Allele: TAGCTACATTTACAGTTAAC TGG |
Inferred Ancestral Allele: Not determined.
AATCAACTATAAATTTAAGATTTAAAATTAAATTTTAATTATGGCCAATAAGTTGAAAAGCAAACGATGCAGCTTATTGTTTGGTCATGCTGTGAGTCCA[AAGCTACATTTACAGTTAACTGG/TAGCTACATTTACAGTTAACTGG,A]
GATTTGCCAATTAATTTTAACTCCTCGGTTAAGATGTATATGCCCAATATCTTTTAGCATGCATGAGTATGTTTAGTGGTGGGATCGTGGTAGTATATGC
GCATATACTACCACGATCCCACCACTAAACATACTCATGCATGCTAAAAGATATTGGGCATATACATCTTAACCGAGGAGTTAAAATTAATTGGCAAATC[CCAGTTAACTGTAAATGTAGCTT/CCAGTTAACTGTAAATGTAGCTA,T]
TGGACTCACAGCATGACCAAACAATAAGCTGCATCGTTTGCTTTTCAACTTATTGGCCATAATTAAAATTTAATTTTAAATCTTAAATTTATAGTTGATT
Populations | Population Size | Frequency of AAGCTACATTTACAGTTAAC TGG(primary allele) | Frequency of TAGCTACATTTACAGTTAAC TGG(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 88.00% | 12.00% | 0.04% | 0.00% | NA |
All Indica | 2759 | 92.50% | 7.50% | 0.04% | 0.00% | NA |
All Japonica | 1512 | 81.20% | 18.70% | 0.07% | 0.00% | NA |
Aus | 269 | 91.40% | 8.60% | 0.00% | 0.00% | NA |
Indica I | 595 | 98.20% | 1.70% | 0.17% | 0.00% | NA |
Indica II | 465 | 92.30% | 7.70% | 0.00% | 0.00% | NA |
Indica III | 913 | 88.70% | 11.30% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 92.70% | 7.30% | 0.00% | 0.00% | NA |
Temperate Japonica | 767 | 94.00% | 6.00% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 63.30% | 36.70% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 78.00% | 21.60% | 0.41% | 0.00% | NA |
VI/Aromatic | 96 | 62.50% | 37.50% | 0.00% | 0.00% | NA |
Intermediate | 90 | 80.00% | 20.00% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg1217642122 | AAGCTACATTTACAGTTAACTGG -> A | LOC_Os12g29580-LOC_Os12g29590 | intergenic_region ; MODIFIER | N | Average:58.326; most accessible tissue: Zhenshan97 root, score: 76.035 | N | N | N | N |
vg1217642122 | AAGCTACATTTACAGTTAACTGG -> TAGCTACATTTACAGTTAACTGG | LOC_Os12g29580-LOC_Os12g29590 | intergenic_region ; MODIFIER | silent_mutation | Average:58.326; most accessible tissue: Zhenshan97 root, score: 76.035 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg1217642122 | NA | 3.39E-06 | mr1171 | 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 |
vg1217642122 | NA | 1.88E-06 | mr1192 | 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 |
vg1217642122 | NA | 3.53E-07 | mr1206 | 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 |
vg1217642122 | NA | 4.39E-06 | mr1324 | 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 |
vg1217642122 | NA | 4.17E-06 | mr1335 | 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 |
vg1217642122 | NA | 1.63E-06 | mr1338 | 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 |
vg1217642122 | 6.90E-07 | 6.35E-10 | mr1565 | 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 |
vg1217642122 | NA | 1.05E-06 | mr1786 | 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 |