| Variant ID: vg0816447617 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr08 | Position: 16447617 |
| Reference Allele: G | Alternative Allele: GTTT,GT,GTT,T,C,GTTTT |
| Primary Allele: G | Secondary Allele: GTTT |
Inferred Ancestral Allele: Not determined.
AGTGCGTCTTCGAGCTCCAGCCGCCAGCCGAGCCGAGTCGGCTGCCATGCCGAGCCGCCTTGCCGCGCCGAATCCGCCCCAATCTCTCCCCTTTTCTTCC[G/GTTT,GT,GTT,T,C,GTTTT]
TTTTTTTGAGGGGTTTTTATCCTCTCATCTTCCTCTATCCTTACCCCCAAAAATCGGAGCAAATCGTTGAGTATTTTATCCGAATCGAACTCGTTTTGAA
TTCAAAACGAGTTCGATTCGGATAAAATACTCAACGATTTGCTCCGATTTTTGGGGGTAAGGATAGAGGAAGATGAGAGGATAAAAACCCCTCAAAAAAA[C/AAAC,AC,AAC,A,G,AAAAC]
GGAAGAAAAGGGGAGAGATTGGGGCGGATTCGGCGCGGCAAGGCGGCTCGGCATGGCAGCCGACTCGGCTCGGCTGGCGGCTGGAGCTCGAAGACGCACT
| Populations | Population Size | Frequency of G(primary allele) | Frequency of GTTT(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 22.80% | 22.20% | 17.99% | 0.02% | GT: 14.60%; C: 12.51%; T: 5.48%; GTT: 4.34%; GTTTT: 0.04% |
| All Indica | 2759 | 1.80% | 37.20% | 29.68% | 0.04% | GT: 11.38%; C: 11.24%; GTT: 7.00%; T: 1.52%; GTTTT: 0.07% |
| All Japonica | 1512 | 66.30% | 0.60% | 0.46% | 0.00% | GT: 19.11%; T: 7.74%; C: 5.82% |
| Aus | 269 | 0.40% | 0.40% | 1.12% | 0.00% | C: 64.31%; T: 33.46%; GT: 0.37% |
| Indica I | 595 | 2.00% | 31.60% | 32.27% | 0.00% | C: 23.70%; GT: 4.37%; T: 3.70%; GTT: 2.35% |
| Indica II | 465 | 1.90% | 35.50% | 41.72% | 0.22% | GTT: 15.70%; GT: 3.87%; C: 1.08% |
| Indica III | 913 | 1.90% | 41.80% | 20.70% | 0.00% | GT: 21.14%; C: 7.78%; GTT: 5.26%; T: 1.20%; GTTTT: 0.22% |
| Indica Intermediate | 786 | 1.70% | 37.20% | 31.04% | 0.00% | C: 11.83%; GT: 9.80%; GTT: 7.38%; T: 1.15% |
| Temperate Japonica | 767 | 69.10% | 0.90% | 0.26% | 0.00% | GT: 29.60%; C: 0.13% |
| Tropical Japonica | 504 | 64.50% | 0.40% | 0.20% | 0.00% | T: 17.46%; C: 15.48%; GT: 1.98% |
| Japonica Intermediate | 241 | 61.00% | 0.00% | 1.66% | 0.00% | GT: 21.58%; T: 12.03%; C: 3.73% |
| VI/Aromatic | 96 | 1.00% | 0.00% | 2.08% | 0.00% | GT: 78.12%; GTT: 9.38%; C: 8.33%; T: 1.04% |
| Intermediate | 90 | 24.40% | 15.60% | 21.11% | 0.00% | C: 13.33%; GT: 12.22%; T: 10.00%; GTT: 3.33% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0816447617 | G -> GTTT | LOC_Os08g26940.1 | upstream_gene_variant ; 3289.0bp to feature; MODIFIER | silent_mutation | Average:57.419; most accessible tissue: Zhenshan97 flag leaf, score: 85.514 | N | N | N | N |
| vg0816447617 | G -> GTTT | LOC_Os08g26950.1 | upstream_gene_variant ; 4460.0bp to feature; MODIFIER | silent_mutation | Average:57.419; most accessible tissue: Zhenshan97 flag leaf, score: 85.514 | N | N | N | N |
| vg0816447617 | G -> GTTT | LOC_Os08g26940-LOC_Os08g26950 | intergenic_region ; MODIFIER | silent_mutation | Average:57.419; most accessible tissue: Zhenshan97 flag leaf, score: 85.514 | N | N | N | N |
| vg0816447617 | G -> C | LOC_Os08g26940.1 | upstream_gene_variant ; 3288.0bp to feature; MODIFIER | silent_mutation | Average:57.419; most accessible tissue: Zhenshan97 flag leaf, score: 85.514 | N | N | N | N |
| vg0816447617 | G -> C | LOC_Os08g26950.1 | upstream_gene_variant ; 4461.0bp to feature; MODIFIER | silent_mutation | Average:57.419; most accessible tissue: Zhenshan97 flag leaf, score: 85.514 | N | N | N | N |
| vg0816447617 | G -> C | LOC_Os08g26940-LOC_Os08g26950 | intergenic_region ; MODIFIER | silent_mutation | Average:57.419; most accessible tissue: Zhenshan97 flag leaf, score: 85.514 | N | N | N | N |
| vg0816447617 | G -> GT | LOC_Os08g26940.1 | upstream_gene_variant ; 3289.0bp to feature; MODIFIER | silent_mutation | Average:57.419; most accessible tissue: Zhenshan97 flag leaf, score: 85.514 | N | N | N | N |
| vg0816447617 | G -> GT | LOC_Os08g26950.1 | upstream_gene_variant ; 4460.0bp to feature; MODIFIER | silent_mutation | Average:57.419; most accessible tissue: Zhenshan97 flag leaf, score: 85.514 | N | N | N | N |
| vg0816447617 | G -> GT | LOC_Os08g26940-LOC_Os08g26950 | intergenic_region ; MODIFIER | silent_mutation | Average:57.419; most accessible tissue: Zhenshan97 flag leaf, score: 85.514 | N | N | N | N |
| vg0816447617 | G -> GTTTT | LOC_Os08g26940.1 | upstream_gene_variant ; 3289.0bp to feature; MODIFIER | silent_mutation | Average:57.419; most accessible tissue: Zhenshan97 flag leaf, score: 85.514 | N | N | N | N |
| vg0816447617 | G -> GTTTT | LOC_Os08g26950.1 | upstream_gene_variant ; 4460.0bp to feature; MODIFIER | silent_mutation | Average:57.419; most accessible tissue: Zhenshan97 flag leaf, score: 85.514 | N | N | N | N |
| vg0816447617 | G -> GTTTT | LOC_Os08g26940-LOC_Os08g26950 | intergenic_region ; MODIFIER | silent_mutation | Average:57.419; most accessible tissue: Zhenshan97 flag leaf, score: 85.514 | N | N | N | N |
| vg0816447617 | G -> DEL | N | N | silent_mutation | Average:57.419; most accessible tissue: Zhenshan97 flag leaf, score: 85.514 | N | N | N | N |
| vg0816447617 | G -> T | LOC_Os08g26940.1 | upstream_gene_variant ; 3288.0bp to feature; MODIFIER | silent_mutation | Average:57.419; most accessible tissue: Zhenshan97 flag leaf, score: 85.514 | N | N | N | N |
| vg0816447617 | G -> T | LOC_Os08g26950.1 | upstream_gene_variant ; 4461.0bp to feature; MODIFIER | silent_mutation | Average:57.419; most accessible tissue: Zhenshan97 flag leaf, score: 85.514 | N | N | N | N |
| vg0816447617 | G -> T | LOC_Os08g26940-LOC_Os08g26950 | intergenic_region ; MODIFIER | silent_mutation | Average:57.419; most accessible tissue: Zhenshan97 flag leaf, score: 85.514 | N | N | N | N |
| vg0816447617 | G -> GTT | LOC_Os08g26940.1 | upstream_gene_variant ; 3289.0bp to feature; MODIFIER | silent_mutation | Average:57.419; most accessible tissue: Zhenshan97 flag leaf, score: 85.514 | N | N | N | N |
| vg0816447617 | G -> GTT | LOC_Os08g26950.1 | upstream_gene_variant ; 4460.0bp to feature; MODIFIER | silent_mutation | Average:57.419; most accessible tissue: Zhenshan97 flag leaf, score: 85.514 | N | N | N | N |
| vg0816447617 | G -> GTT | LOC_Os08g26940-LOC_Os08g26950 | intergenic_region ; MODIFIER | silent_mutation | Average:57.419; most accessible tissue: Zhenshan97 flag leaf, score: 85.514 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0816447617 | NA | 1.64E-06 | mr1073 | 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 |
| vg0816447617 | NA | 6.01E-07 | mr1076 | 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 |
| vg0816447617 | NA | 2.60E-07 | mr1082 | 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 |
| vg0816447617 | NA | 2.88E-06 | mr1083 | 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 |
| vg0816447617 | NA | 9.63E-07 | mr1226 | 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 |
| vg0816447617 | 2.70E-07 | 6.31E-09 | mr1227 | 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 |
| vg0816447617 | NA | 5.12E-09 | mr1348 | 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 |
| vg0816447617 | NA | 5.19E-08 | mr1349 | 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 |
| vg0816447617 | 8.75E-06 | 6.11E-08 | mr1411 | 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 |
| vg0816447617 | NA | 3.07E-06 | mr1560 | 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 |
| vg0816447617 | NA | 1.94E-08 | mr1942 | 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 |
| vg0816447617 | NA | 3.92E-06 | mr1082_2 | 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 |
| vg0816447617 | NA | 3.98E-06 | mr1107_2 | 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 |
| vg0816447617 | NA | 4.02E-06 | mr1226_2 | 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 |