| Variant ID: vg1011030483 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr10 | Position: 11030483 |
| Reference Allele: C | Alternative Allele: A,G,CTCCCTCTGATTTCATTTCAATTGACG,CTCCCTCTGATTTCATTTCAATTGACGTT,CTCCCTCTGATTTCAT,CTCCCTCTGATTTCATTTCAATTGACGT |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
TATGACCTGCAGCCCCAGAGGCAGTTCCCAGCAGGTCCGGTGGCCGCCCGGGCTTCGTTGTTGCCATCTTTACTGTCGAAAGCCATCAAAATCTATAAAA[C/A,G,CTCCCTCTGATTTCATTTCAATTGACG,CTCCCTCTGATTTCATTTCAATTGACGTT,CTCCCTCTGATTTCAT,CTCCCTCTGATTTCATTTCAATTGACGT]
TTAGTCGATCATAGTAAAATATCATTAGCTAACATTGATTAATTCGGTGCTAAATAGCCTCCCATTGTATATGATGTCCTTCTTTGCCATACCAAGAGGG
CCCTCTTGGTATGGCAAAGAAGGACATCATATACAATGGGAGGCTATTTAGCACCGAATTAATCAATGTTAGCTAATGATATTTTACTATGATCGACTAA[G/T,C,CGTCAATTGAAATGAAATCAGAGGGAG,AACGTCAATTGAAATGAAATCAGAGGGAG,ATGAAATCAGAGGGAG,ACGTCAATTGAAATGAAATCAGAGGGAG]
TTTTATAGATTTTGATGGCTTTCGACAGTAAAGATGGCAACAACGAAGCCCGGGCGGCCACCGGACCTGCTGGGAACTGCCTCTGGGGCTGCAGGTCATA
| Populations | Population Size | Frequency of A(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 76.60% | 4.30% | 14.37% | 2.43% | G: 1.04%; CTCCCTCTGATTTCATTTCAATTGACGTT: 0.47%; CTCCCTCTGATTTCATTTCAATTGACG: 0.34%; CTCCCTCTGATTTCATTTCAATTGACGT: 0.23%; CTCCCTCTGATTTCAT: 0.23% |
| All Indica | 2759 | 92.40% | 0.20% | 4.42% | 0.94% | G: 1.78%; CTCCCTCTGATTTCAT: 0.11%; CTCCCTCTGATTTCATTTCAATTGACGT: 0.07%; CTCCCTCTGATTTCATTTCAATTGACG: 0.04%; CTCCCTCTGATTTCATTTCAATTGACGTT: 0.04% |
| All Japonica | 1512 | 59.20% | 12.80% | 22.82% | 2.78% | CTCCCTCTGATTTCATTTCAATTGACGTT: 1.06%; CTCCCTCTGATTTCATTTCAATTGACGT: 0.53%; CTCCCTCTGATTTCATTTCAATTGACG: 0.53%; CTCCCTCTGATTTCAT: 0.33% |
| Aus | 269 | 26.80% | 0.00% | 56.13% | 12.64% | CTCCCTCTGATTTCATTTCAATTGACG: 2.23%; CTCCCTCTGATTTCATTTCAATTGACGTT: 1.12%; CTCCCTCTGATTTCAT: 0.74%; CTCCCTCTGATTTCATTTCAATTGACGT: 0.37% |
| Indica I | 595 | 87.60% | 0.70% | 8.40% | 0.00% | G: 3.36% |
| Indica II | 465 | 98.30% | 0.20% | 0.65% | 0.00% | G: 0.86% |
| Indica III | 913 | 94.30% | 0.00% | 2.74% | 1.20% | G: 1.20%; CTCCCTCTGATTTCATTTCAATTGACGT: 0.22%; CTCCCTCTGATTTCAT: 0.22%; CTCCCTCTGATTTCATTTCAATTGACGTT: 0.11% |
| Indica Intermediate | 786 | 90.50% | 0.00% | 5.60% | 1.91% | G: 1.78%; CTCCCTCTGATTTCATTTCAATTGACG: 0.13%; CTCCCTCTGATTTCAT: 0.13% |
| Temperate Japonica | 767 | 63.10% | 23.90% | 11.73% | 1.04% | CTCCCTCTGATTTCATTTCAATTGACG: 0.13%; CTCCCTCTGATTTCATTTCAATTGACGTT: 0.13% |
| Tropical Japonica | 504 | 47.20% | 1.20% | 39.48% | 6.15% | CTCCCTCTGATTTCATTTCAATTGACGTT: 2.78%; CTCCCTCTGATTTCATTTCAATTGACG: 1.19%; CTCCCTCTGATTTCATTTCAATTGACGT: 1.19%; CTCCCTCTGATTTCAT: 0.79% |
| Japonica Intermediate | 241 | 71.80% | 1.70% | 23.24% | 1.24% | CTCCCTCTGATTTCATTTCAATTGACGT: 0.83%; CTCCCTCTGATTTCATTTCAATTGACG: 0.41%; CTCCCTCTGATTTCAT: 0.41%; CTCCCTCTGATTTCATTTCAATTGACGTT: 0.41% |
| VI/Aromatic | 96 | 40.60% | 1.00% | 43.75% | 12.50% | CTCCCTCTGATTTCAT: 1.04%; CTCCCTCTGATTTCATTTCAATTGACG: 1.04% |
| Intermediate | 90 | 73.30% | 2.20% | 21.11% | 1.11% | CTCCCTCTGATTTCATTTCAATTGACGTT: 2.22% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1011030483 | C -> CTCCCTCTGATTTCATTTCAATTGACGT | LOC_Os10g21550.1 | upstream_gene_variant ; 3458.0bp to feature; MODIFIER | silent_mutation | Average:63.852; most accessible tissue: Minghui63 panicle, score: 84.005 | N | N | N | N |
| vg1011030483 | C -> CTCCCTCTGATTTCATTTCAATTGACGT | LOC_Os10g21540.1 | downstream_gene_variant ; 991.0bp to feature; MODIFIER | silent_mutation | Average:63.852; most accessible tissue: Minghui63 panicle, score: 84.005 | N | N | N | N |
| vg1011030483 | C -> CTCCCTCTGATTTCATTTCAATTGACGT | LOC_Os10g21560.1 | downstream_gene_variant ; 4979.0bp to feature; MODIFIER | silent_mutation | Average:63.852; most accessible tissue: Minghui63 panicle, score: 84.005 | N | N | N | N |
| vg1011030483 | C -> CTCCCTCTGATTTCATTTCAATTGACGT | LOC_Os10g21560.2 | downstream_gene_variant ; 4979.0bp to feature; MODIFIER | silent_mutation | Average:63.852; most accessible tissue: Minghui63 panicle, score: 84.005 | N | N | N | N |
| vg1011030483 | C -> CTCCCTCTGATTTCATTTCAATTGACGT | LOC_Os10g21540-LOC_Os10g21550 | intergenic_region ; MODIFIER | silent_mutation | Average:63.852; most accessible tissue: Minghui63 panicle, score: 84.005 | N | N | N | N |
| vg1011030483 | C -> G | LOC_Os10g21550.1 | upstream_gene_variant ; 3459.0bp to feature; MODIFIER | silent_mutation | Average:63.852; most accessible tissue: Minghui63 panicle, score: 84.005 | N | N | N | N |
| vg1011030483 | C -> G | LOC_Os10g21540.1 | downstream_gene_variant ; 990.0bp to feature; MODIFIER | silent_mutation | Average:63.852; most accessible tissue: Minghui63 panicle, score: 84.005 | N | N | N | N |
| vg1011030483 | C -> G | LOC_Os10g21560.1 | downstream_gene_variant ; 4980.0bp to feature; MODIFIER | silent_mutation | Average:63.852; most accessible tissue: Minghui63 panicle, score: 84.005 | N | N | N | N |
| vg1011030483 | C -> G | LOC_Os10g21560.2 | downstream_gene_variant ; 4980.0bp to feature; MODIFIER | silent_mutation | Average:63.852; most accessible tissue: Minghui63 panicle, score: 84.005 | N | N | N | N |
| vg1011030483 | C -> G | LOC_Os10g21540-LOC_Os10g21550 | intergenic_region ; MODIFIER | silent_mutation | Average:63.852; most accessible tissue: Minghui63 panicle, score: 84.005 | N | N | N | N |
| vg1011030483 | C -> CTCCCTCTGATTTCATTTCAATTGACG | LOC_Os10g21550.1 | upstream_gene_variant ; 3458.0bp to feature; MODIFIER | silent_mutation | Average:63.852; most accessible tissue: Minghui63 panicle, score: 84.005 | N | N | N | N |
| vg1011030483 | C -> CTCCCTCTGATTTCATTTCAATTGACG | LOC_Os10g21540.1 | downstream_gene_variant ; 991.0bp to feature; MODIFIER | silent_mutation | Average:63.852; most accessible tissue: Minghui63 panicle, score: 84.005 | N | N | N | N |
| vg1011030483 | C -> CTCCCTCTGATTTCATTTCAATTGACG | LOC_Os10g21560.1 | downstream_gene_variant ; 4979.0bp to feature; MODIFIER | silent_mutation | Average:63.852; most accessible tissue: Minghui63 panicle, score: 84.005 | N | N | N | N |
| vg1011030483 | C -> CTCCCTCTGATTTCATTTCAATTGACG | LOC_Os10g21560.2 | downstream_gene_variant ; 4979.0bp to feature; MODIFIER | silent_mutation | Average:63.852; most accessible tissue: Minghui63 panicle, score: 84.005 | N | N | N | N |
| vg1011030483 | C -> CTCCCTCTGATTTCATTTCAATTGACG | LOC_Os10g21540-LOC_Os10g21550 | intergenic_region ; MODIFIER | silent_mutation | Average:63.852; most accessible tissue: Minghui63 panicle, score: 84.005 | N | N | N | N |
| vg1011030483 | C -> DEL | N | N | silent_mutation | Average:63.852; most accessible tissue: Minghui63 panicle, score: 84.005 | N | N | N | N |
| vg1011030483 | C -> CTCCCTCTGATTTCAT | LOC_Os10g21550.1 | upstream_gene_variant ; 3458.0bp to feature; MODIFIER | silent_mutation | Average:63.852; most accessible tissue: Minghui63 panicle, score: 84.005 | N | N | N | N |
| vg1011030483 | C -> CTCCCTCTGATTTCAT | LOC_Os10g21540.1 | downstream_gene_variant ; 991.0bp to feature; MODIFIER | silent_mutation | Average:63.852; most accessible tissue: Minghui63 panicle, score: 84.005 | N | N | N | N |
| vg1011030483 | C -> CTCCCTCTGATTTCAT | LOC_Os10g21560.1 | downstream_gene_variant ; 4979.0bp to feature; MODIFIER | silent_mutation | Average:63.852; most accessible tissue: Minghui63 panicle, score: 84.005 | N | N | N | N |
| vg1011030483 | C -> CTCCCTCTGATTTCAT | LOC_Os10g21560.2 | downstream_gene_variant ; 4979.0bp to feature; MODIFIER | silent_mutation | Average:63.852; most accessible tissue: Minghui63 panicle, score: 84.005 | N | N | N | N |
| vg1011030483 | C -> CTCCCTCTGATTTCAT | LOC_Os10g21540-LOC_Os10g21550 | intergenic_region ; MODIFIER | silent_mutation | Average:63.852; most accessible tissue: Minghui63 panicle, score: 84.005 | N | N | N | N |
| vg1011030483 | C -> CTCCCTCTGATTTCATTTCAATTGACGTT | LOC_Os10g21550.1 | upstream_gene_variant ; 3458.0bp to feature; MODIFIER | silent_mutation | Average:63.852; most accessible tissue: Minghui63 panicle, score: 84.005 | N | N | N | N |
| vg1011030483 | C -> CTCCCTCTGATTTCATTTCAATTGACGTT | LOC_Os10g21540.1 | downstream_gene_variant ; 991.0bp to feature; MODIFIER | silent_mutation | Average:63.852; most accessible tissue: Minghui63 panicle, score: 84.005 | N | N | N | N |
| vg1011030483 | C -> CTCCCTCTGATTTCATTTCAATTGACGTT | LOC_Os10g21560.1 | downstream_gene_variant ; 4979.0bp to feature; MODIFIER | silent_mutation | Average:63.852; most accessible tissue: Minghui63 panicle, score: 84.005 | N | N | N | N |
| vg1011030483 | C -> CTCCCTCTGATTTCATTTCAATTGACGTT | LOC_Os10g21560.2 | downstream_gene_variant ; 4979.0bp to feature; MODIFIER | silent_mutation | Average:63.852; most accessible tissue: Minghui63 panicle, score: 84.005 | N | N | N | N |
| vg1011030483 | C -> CTCCCTCTGATTTCATTTCAATTGACGTT | LOC_Os10g21540-LOC_Os10g21550 | intergenic_region ; MODIFIER | silent_mutation | Average:63.852; most accessible tissue: Minghui63 panicle, score: 84.005 | N | N | N | N |
| vg1011030483 | C -> A | LOC_Os10g21550.1 | upstream_gene_variant ; 3459.0bp to feature; MODIFIER | silent_mutation | Average:63.852; most accessible tissue: Minghui63 panicle, score: 84.005 | N | N | N | N |
| vg1011030483 | C -> A | LOC_Os10g21540.1 | downstream_gene_variant ; 990.0bp to feature; MODIFIER | silent_mutation | Average:63.852; most accessible tissue: Minghui63 panicle, score: 84.005 | N | N | N | N |
| vg1011030483 | C -> A | LOC_Os10g21560.1 | downstream_gene_variant ; 4980.0bp to feature; MODIFIER | silent_mutation | Average:63.852; most accessible tissue: Minghui63 panicle, score: 84.005 | N | N | N | N |
| vg1011030483 | C -> A | LOC_Os10g21560.2 | downstream_gene_variant ; 4980.0bp to feature; MODIFIER | silent_mutation | Average:63.852; most accessible tissue: Minghui63 panicle, score: 84.005 | N | N | N | N |
| vg1011030483 | C -> A | LOC_Os10g21540-LOC_Os10g21550 | intergenic_region ; MODIFIER | silent_mutation | Average:63.852; most accessible tissue: Minghui63 panicle, score: 84.005 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1011030483 | NA | 4.21E-17 | Heading_date | All | Not | Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652 |
| vg1011030483 | NA | 6.56E-14 | Heading_date | Jap_All | Not | Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652 |
| vg1011030483 | NA | 3.23E-06 | mr1042 | 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 |
| vg1011030483 | NA | 6.38E-07 | mr1252 | 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 |
| vg1011030483 | NA | 8.81E-06 | mr1289 | 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 |
| vg1011030483 | NA | 1.55E-08 | mr1549 | 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 |
| vg1011030483 | NA | 6.80E-06 | mr1550 | 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 |
| vg1011030483 | NA | 4.06E-06 | mr1576 | 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 |
| vg1011030483 | 3.14E-07 | NA | mr1677 | 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 |
| vg1011030483 | NA | 2.49E-06 | mr1677 | 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 |
| vg1011030483 | NA | 9.60E-06 | mr1729 | 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 |
| vg1011030483 | NA | 5.33E-07 | mr1729 | 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 |
| vg1011030483 | NA | 7.22E-09 | mr1757 | 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 |
| vg1011030483 | NA | 4.02E-06 | mr1354_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 |
| vg1011030483 | NA | 2.73E-06 | mr1549_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 |
| vg1011030483 | NA | 5.79E-06 | mr1723_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 |
| vg1011030483 | NA | 8.18E-06 | mr1757_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 |