Variant ID: vg0117431722 (JBrowse) | Variation Type: INDEL |
Chromosome: chr01 | Position: 17431722 |
Reference Allele: AACCGGGAAATTCTTCCCGGGTGCACACGAGTGAGGACATCTTCCCGGGTGCACATGAGTGAGGACAAAGTGTGC | Alternative Allele: GACCGGGAAATTCTTCCCGGGTGCACACGAGTGAGGACATCTTCCCGGGTGCACATGAGTGAGGACAAAGTGTGC,A |
Primary Allele: AACCGGGAAATTCTTCCCGG GTGCACACGAGTGAGGACAT CTTCCCGGGTGCACATGAGT GAGGACAAAGTGTGC | Secondary Allele: GACCGGGAAATTCTTCCCGG GTGCACACGAGTGAGGACAT CTTCCCGGGTGCACATGAGT GAGGACAAAGTGTGC |
Inferred Ancestral Allele: Not determined.
TACTCATATCAACAAGTTGCAACTTCTTTTCCGGAATCCAATCTCCAAAGAACTCCAGGGTTAAGCGTGCTTGGCCTGGAGCAATTTGGGATGGGTGACC[AACCGGGAAATTCTTCCCGGGTGCACACGAGTGAGGACATCTTCCCGGGTGCACATGAGTGAGGACAAAGTGTGC/GACCGGGAAATTCTTCCCGGGTGCACACGAGTGAGGACATCTTCCCGGGTGCACATGAGTGAGGACAAAGTGTGC,A]
AGAAAAGATATGTGTTGGTCTGTGAGGGCAGTCTATGACCTCTGAAAGCTATCAGATGTAAGCGGGCCTGGCCTGGGGGAAGGCGGGACGTTACATCCCG
CGGGATGTAACGTCCCGCCTTCCCCCAGGCCAGGCCCGCTTACATCTGATAGCTTTCAGAGGTCATAGACTGCCCTCACAGACCAACACATATCTTTTCT[GCACACTTTGTCCTCACTCATGTGCACCCGGGAAGATGTCCTCACTCGTGTGCACCCGGGAAGAATTTCCCGGTT/GCACACTTTGTCCTCACTCATGTGCACCCGGGAAGATGTCCTCACTCGTGTGCACCCGGGAAGAATTTCCCGGTC,T]
GGTCACCCATCCCAAATTGCTCCAGGCCAAGCACGCTTAACCCTGGAGTTCTTTGGAGATTGGATTCCGGAAAAGAAGTTGCAACTTGTTGATATGAGTA
Populations | Population Size | Frequency of AACCGGGAAATTCTTCCCGG GTGCACACGAGTGAGGACAT CTTCCCGGGTGCACATGAGT GAGGACAAAGTGTGC(primary allele) | Frequency of GACCGGGAAATTCTTCCCGG GTGCACACGAGTGAGGACAT CTTCCCGGGTGCACATGAGT GAGGACAAAGTGTGC(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 91.20% | 1.80% | 5.25% | 1.74% | A: 0.04% |
All Indica | 2759 | 86.80% | 2.10% | 8.26% | 2.83% | NA |
All Japonica | 1512 | 97.30% | 1.50% | 0.99% | 0.07% | A: 0.13% |
Aus | 269 | 99.30% | 0.00% | 0.74% | 0.00% | NA |
Indica I | 595 | 76.10% | 3.70% | 15.13% | 5.04% | NA |
Indica II | 465 | 84.70% | 2.20% | 10.32% | 2.80% | NA |
Indica III | 913 | 92.00% | 2.10% | 4.60% | 1.31% | NA |
Indica Intermediate | 786 | 89.90% | 1.00% | 6.11% | 2.93% | NA |
Temperate Japonica | 767 | 99.30% | 0.30% | 0.39% | 0.00% | NA |
Tropical Japonica | 504 | 97.00% | 0.20% | 2.38% | 0.00% | A: 0.40% |
Japonica Intermediate | 241 | 91.30% | 8.30% | 0.00% | 0.41% | NA |
VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Intermediate | 90 | 91.10% | 2.20% | 3.33% | 3.33% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0117431722 | AACCGGGAAATTCTTCCCGGGTGCACACGAGTGAGGACATCTTCCCGGGTGCACATGAGTGAGGACAAAGTGTGC -> A | LOC_Os01g31810.2 | upstream_gene_variant ; 2330.0bp to feature; MODIFIER | silent_mutation | Average:28.834; most accessible tissue: Zhenshan97 panicle, score: 57.341 | N | N | N | N |
vg0117431722 | AACCGGGAAATTCTTCCCGGGTGCACACGAGTGAGGACATCTTCCCGGGTGCACATGAGTGAGGACAAAGTGTGC -> A | LOC_Os01g31820.1 | upstream_gene_variant ; 1139.0bp to feature; MODIFIER | silent_mutation | Average:28.834; most accessible tissue: Zhenshan97 panicle, score: 57.341 | N | N | N | N |
vg0117431722 | AACCGGGAAATTCTTCCCGGGTGCACACGAGTGAGGACATCTTCCCGGGTGCACATGAGTGAGGACAAAGTGTGC -> A | LOC_Os01g31830.1 | downstream_gene_variant ; 4051.0bp to feature; MODIFIER | silent_mutation | Average:28.834; most accessible tissue: Zhenshan97 panicle, score: 57.341 | N | N | N | N |
vg0117431722 | AACCGGGAAATTCTTCCCGGGTGCACACGAGTGAGGACATCTTCCCGGGTGCACATGAGTGAGGACAAAGTGTGC -> A | LOC_Os01g31810-LOC_Os01g31820 | intergenic_region ; MODIFIER | silent_mutation | Average:28.834; most accessible tissue: Zhenshan97 panicle, score: 57.341 | N | N | N | N |
vg0117431722 | AACCGGGAAATTCTTCCCGGGTGCACACGAGTGAGGACATCTTCCCGGGTGCACATGAGTGAGGACAAAGTGTGC -> GACCGGGAAATTCTTCCCGGGTGCACACGA GTGAGGACATCTTCCCGGGTGCACATGAGT GAGGACAAAGTGTGC | LOC_Os01g31810.2 | upstream_gene_variant ; 2329.0bp to feature; MODIFIER | silent_mutation | Average:28.834; most accessible tissue: Zhenshan97 panicle, score: 57.341 | N | N | N | N |
vg0117431722 | AACCGGGAAATTCTTCCCGGGTGCACACGAGTGAGGACATCTTCCCGGGTGCACATGAGTGAGGACAAAGTGTGC -> GACCGGGAAATTCTTCCCGGGTGCACACGA GTGAGGACATCTTCCCGGGTGCACATGAGT GAGGACAAAGTGTGC | LOC_Os01g31820.1 | upstream_gene_variant ; 1140.0bp to feature; MODIFIER | silent_mutation | Average:28.834; most accessible tissue: Zhenshan97 panicle, score: 57.341 | N | N | N | N |
vg0117431722 | AACCGGGAAATTCTTCCCGGGTGCACACGAGTGAGGACATCTTCCCGGGTGCACATGAGTGAGGACAAAGTGTGC -> GACCGGGAAATTCTTCCCGGGTGCACACGA GTGAGGACATCTTCCCGGGTGCACATGAGT GAGGACAAAGTGTGC | LOC_Os01g31830.1 | downstream_gene_variant ; 4052.0bp to feature; MODIFIER | silent_mutation | Average:28.834; most accessible tissue: Zhenshan97 panicle, score: 57.341 | N | N | N | N |
vg0117431722 | AACCGGGAAATTCTTCCCGGGTGCACACGAGTGAGGACATCTTCCCGGGTGCACATGAGTGAGGACAAAGTGTGC -> GACCGGGAAATTCTTCCCGGGTGCACACGA GTGAGGACATCTTCCCGGGTGCACATGAGT GAGGACAAAGTGTGC | LOC_Os01g31810-LOC_Os01g31820 | intergenic_region ; MODIFIER | silent_mutation | Average:28.834; most accessible tissue: Zhenshan97 panicle, score: 57.341 | N | N | N | N |
vg0117431722 | AACCGGGAAATTCTTCCCGGGTGCACACGAGTGAGGACATCTTCCCGGGTGCACATGAGTGAGGACAAAGTGTGC -> DEL | N | N | silent_mutation | Average:28.834; most accessible tissue: Zhenshan97 panicle, score: 57.341 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0117431722 | 9.71E-06 | NA | mr1613_2 | 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 |
vg0117431722 | 1.36E-08 | NA | mr1613_2 | Ind_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 |