| Variant ID: vg0519396234 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr05 | Position: 19396234 |
| Reference Allele: T | Alternative Allele: TGTGTATAGTTTTTTTTTAAGG,TGTGTATAGTTTTTTTTAAGG,G,TTGTGTATAGTTTTTTTTTAAGG,TGTGTATAGTTTTTTTTTTAAGG |
| Primary Allele: TGTGTATAGTTTTTTTTTAA GG | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TACTTGGCCCTGCCATTCCAGTACTCACCAAGCAGACACGTCGCCCTTATTATGTACTCCTAGGAGTACCACCAGTAGGTTACTGCAGTTTTCGATTAAG[T/TGTGTATAGTTTTTTTTTAAGG,TGTGTATAGTTTTTTTTAAGG,G,TTGTGTATAGTTTTTTTTTAAGG,TGTGTATAGTTTTTTTTTTAAGG]
CTTTGAAGTATACACATTTAAAGTATTAAAAGTAGACTAATAATAAAATAAATTACAGATTCCGCCTGTAAACTGTGAGATAAATTTATTAAGTCTAATT
AATTAGACTTAATAAATTTATCTCACAGTTTACAGGCGGAATCTGTAATTTATTTTATTATTAGTCTACTTTTAATACTTTAAATGTGTATACTTCAAAG[A/CCTTAAAAAAAAACTATACACA,CCTTAAAAAAAACTATACACA,C,CCTTAAAAAAAAACTATACACAA,CCTTAAAAAAAAAACTATACACA]
CTTAATCGAAAACTGCAGTAACCTACTGGTGGTACTCCTAGGAGTACATAATAAGGGCGACGTGTCTGCTTGGTGAGTACTGGAATGGCAGGGCCAAGTA
| Populations | Population Size | Frequency of TGTGTATAGTTTTTTTTTAA GG(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 33.10% | 23.30% | 9.27% | 32.54% | G: 1.61%; TTGTGTATAGTTTTTTTTTAAGG: 0.06%; TGTGTATAGTTTTTTTTAAGG: 0.06% |
| All Indica | 2759 | 41.40% | 4.00% | 6.45% | 47.81% | G: 0.18%; TTGTGTATAGTTTTTTTTTAAGG: 0.11%; TGTGTATAGTTTTTTTTAAGG: 0.04% |
| All Japonica | 1512 | 2.30% | 63.20% | 16.67% | 13.10% | G: 4.70% |
| Aus | 269 | 95.20% | 2.20% | 1.86% | 0.00% | TGTGTATAGTTTTTTTTAAGG: 0.74% |
| Indica I | 595 | 19.20% | 2.40% | 2.69% | 75.63% | G: 0.17% |
| Indica II | 465 | 71.20% | 4.30% | 2.80% | 21.72% | NA |
| Indica III | 913 | 37.10% | 3.20% | 8.87% | 50.27% | TTGTGTATAGTTTTTTTTTAAGG: 0.33%; G: 0.11%; TGTGTATAGTTTTTTTTAAGG: 0.11% |
| Indica Intermediate | 786 | 45.50% | 6.10% | 8.65% | 39.31% | G: 0.38% |
| Temperate Japonica | 767 | 3.10% | 70.50% | 20.73% | 2.09% | G: 3.52% |
| Tropical Japonica | 504 | 0.80% | 56.90% | 7.94% | 29.56% | G: 4.76% |
| Japonica Intermediate | 241 | 2.90% | 53.10% | 21.99% | 13.69% | G: 8.30% |
| VI/Aromatic | 96 | 93.80% | 5.20% | 0.00% | 1.04% | NA |
| Intermediate | 90 | 47.80% | 26.70% | 3.33% | 22.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0519396234 | T -> TGTGTATAGTTTTTTTTAAGG | LOC_Os05g33080.1 | upstream_gene_variant ; 2671.0bp to feature; MODIFIER | silent_mutation | Average:69.724; most accessible tissue: Callus, score: 88.566 | N | N | N | N |
| vg0519396234 | T -> TGTGTATAGTTTTTTTTAAGG | LOC_Os05g33070.1 | downstream_gene_variant ; 825.0bp to feature; MODIFIER | silent_mutation | Average:69.724; most accessible tissue: Callus, score: 88.566 | N | N | N | N |
| vg0519396234 | T -> TGTGTATAGTTTTTTTTAAGG | LOC_Os05g33070-LOC_Os05g33080 | intergenic_region ; MODIFIER | silent_mutation | Average:69.724; most accessible tissue: Callus, score: 88.566 | N | N | N | N |
| vg0519396234 | T -> DEL | N | N | silent_mutation | Average:69.724; most accessible tissue: Callus, score: 88.566 | N | N | N | N |
| vg0519396234 | T -> TTGTGTATAGTTTTTTTTTAAGG | LOC_Os05g33080.1 | upstream_gene_variant ; 2671.0bp to feature; MODIFIER | silent_mutation | Average:69.724; most accessible tissue: Callus, score: 88.566 | N | N | N | N |
| vg0519396234 | T -> TTGTGTATAGTTTTTTTTTAAGG | LOC_Os05g33070.1 | downstream_gene_variant ; 825.0bp to feature; MODIFIER | silent_mutation | Average:69.724; most accessible tissue: Callus, score: 88.566 | N | N | N | N |
| vg0519396234 | T -> TTGTGTATAGTTTTTTTTTAAGG | LOC_Os05g33070-LOC_Os05g33080 | intergenic_region ; MODIFIER | silent_mutation | Average:69.724; most accessible tissue: Callus, score: 88.566 | N | N | N | N |
| vg0519396234 | T -> G | LOC_Os05g33080.1 | upstream_gene_variant ; 2672.0bp to feature; MODIFIER | silent_mutation | Average:69.724; most accessible tissue: Callus, score: 88.566 | N | N | N | N |
| vg0519396234 | T -> G | LOC_Os05g33070.1 | downstream_gene_variant ; 824.0bp to feature; MODIFIER | silent_mutation | Average:69.724; most accessible tissue: Callus, score: 88.566 | N | N | N | N |
| vg0519396234 | T -> G | LOC_Os05g33070-LOC_Os05g33080 | intergenic_region ; MODIFIER | silent_mutation | Average:69.724; most accessible tissue: Callus, score: 88.566 | N | N | N | N |
| vg0519396234 | T -> TGTGTATAGTTTTTTTTTTAAGG | LOC_Os05g33080.1 | upstream_gene_variant ; 2671.0bp to feature; MODIFIER | N | Average:69.724; most accessible tissue: Callus, score: 88.566 | N | N | N | N |
| vg0519396234 | T -> TGTGTATAGTTTTTTTTTTAAGG | LOC_Os05g33070.1 | downstream_gene_variant ; 825.0bp to feature; MODIFIER | N | Average:69.724; most accessible tissue: Callus, score: 88.566 | N | N | N | N |
| vg0519396234 | T -> TGTGTATAGTTTTTTTTTTAAGG | LOC_Os05g33070-LOC_Os05g33080 | intergenic_region ; MODIFIER | N | Average:69.724; most accessible tissue: Callus, score: 88.566 | N | N | N | N |
| vg0519396234 | T -> TGTGTATAGTTTTTTTTTAAGG | LOC_Os05g33080.1 | upstream_gene_variant ; 2671.0bp to feature; MODIFIER | silent_mutation | Average:69.724; most accessible tissue: Callus, score: 88.566 | N | N | N | N |
| vg0519396234 | T -> TGTGTATAGTTTTTTTTTAAGG | LOC_Os05g33070.1 | downstream_gene_variant ; 825.0bp to feature; MODIFIER | silent_mutation | Average:69.724; most accessible tissue: Callus, score: 88.566 | N | N | N | N |
| vg0519396234 | T -> TGTGTATAGTTTTTTTTTAAGG | LOC_Os05g33070-LOC_Os05g33080 | intergenic_region ; MODIFIER | silent_mutation | Average:69.724; most accessible tissue: Callus, score: 88.566 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0519396234 | NA | 5.00E-12 | mr1232 | 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 |
| vg0519396234 | NA | 6.05E-18 | mr1557 | 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 |
| vg0519396234 | NA | 6.02E-10 | mr1565 | 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 |
| vg0519396234 | NA | 8.02E-06 | mr1715 | 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 |
| vg0519396234 | NA | 2.04E-07 | mr1174_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 |
| vg0519396234 | NA | 6.21E-06 | mr1188_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 |
| vg0519396234 | NA | 3.61E-11 | mr1232_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 |
| vg0519396234 | NA | 6.55E-07 | mr1347_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 |
| vg0519396234 | NA | 2.35E-18 | mr1557_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 |
| vg0519396234 | NA | 1.94E-10 | mr1565_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 |
| vg0519396234 | NA | 6.37E-06 | mr1633_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 |
| vg0519396234 | NA | 4.01E-20 | mr1715_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 |
| vg0519396234 | 4.79E-06 | 4.79E-06 | mr1828_2 | Jap_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 |