| Variant ID: vg1222419971 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr12 | Position: 22419971 |
| Reference Allele: G | Alternative Allele: A,GT |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TATGATTTGACAATGTGATGCTACCGTAAATATTTGCTAATGACAGATTAATTAGGCTTAATAGATTCGTCTCGCAGTTTATATGCGGAATTTATAATTT[G/A,GT]
TTTTGTTATTAGTCTACATTTAATACTTTAAATATGTTTCTGTATACTTAAAAAAGATTTGGCACACGAACTAAACACAGCCTAAATAAAGTGCTCAAGA
TCTTGAGCACTTTATTTAGGCTGTGTTTAGTTCGTGTGCCAAATCTTTTTTAAGTATACAGAAACATATTTAAAGTATTAAATGTAGACTAATAACAAAA[C/T,AC]
AAATTATAAATTCCGCATATAAACTGCGAGACGAATCTATTAAGCCTAATTAATCTGTCATTAGCAAATATTTACGGTAGCATCACATTGTCAAATCATA
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 43.20% | 13.60% | 0.78% | 42.42% | GT: 0.02% |
| All Indica | 2759 | 33.60% | 6.50% | 1.12% | 58.72% | GT: 0.04% |
| All Japonica | 1512 | 68.40% | 18.50% | 0.26% | 12.90% | NA |
| Aus | 269 | 6.30% | 30.10% | 0.74% | 62.83% | NA |
| Indica I | 595 | 34.80% | 8.20% | 0.84% | 55.97% | GT: 0.17% |
| Indica II | 465 | 22.80% | 0.00% | 1.29% | 75.91% | NA |
| Indica III | 913 | 37.00% | 8.20% | 1.10% | 53.67% | NA |
| Indica Intermediate | 786 | 35.10% | 7.10% | 1.27% | 56.49% | NA |
| Temperate Japonica | 767 | 77.30% | 14.00% | 0.13% | 8.60% | NA |
| Tropical Japonica | 504 | 66.90% | 11.90% | 0.40% | 20.83% | NA |
| Japonica Intermediate | 241 | 43.20% | 46.50% | 0.41% | 9.96% | NA |
| VI/Aromatic | 96 | 10.40% | 85.40% | 0.00% | 4.17% | NA |
| Intermediate | 90 | 60.00% | 21.10% | 0.00% | 18.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1222419971 | G -> GT | LOC_Os12g36600.1 | downstream_gene_variant ; 4356.0bp to feature; MODIFIER | silent_mutation | Average:10.616; most accessible tissue: Callus, score: 63.722 | N | N | N | N |
| vg1222419971 | G -> GT | LOC_Os12g36610.1 | downstream_gene_variant ; 707.0bp to feature; MODIFIER | silent_mutation | Average:10.616; most accessible tissue: Callus, score: 63.722 | N | N | N | N |
| vg1222419971 | G -> GT | LOC_Os12g36620.1 | intron_variant ; MODIFIER | silent_mutation | Average:10.616; most accessible tissue: Callus, score: 63.722 | N | N | N | N |
| vg1222419971 | G -> A | LOC_Os12g36600.1 | downstream_gene_variant ; 4355.0bp to feature; MODIFIER | silent_mutation | Average:10.616; most accessible tissue: Callus, score: 63.722 | N | N | N | N |
| vg1222419971 | G -> A | LOC_Os12g36610.1 | downstream_gene_variant ; 706.0bp to feature; MODIFIER | silent_mutation | Average:10.616; most accessible tissue: Callus, score: 63.722 | N | N | N | N |
| vg1222419971 | G -> A | LOC_Os12g36620.1 | intron_variant ; MODIFIER | silent_mutation | Average:10.616; most accessible tissue: Callus, score: 63.722 | N | N | N | N |
| vg1222419971 | G -> DEL | N | N | silent_mutation | Average:10.616; most accessible tissue: Callus, score: 63.722 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1222419971 | NA | 9.34E-07 | mr1057 | 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 |
| vg1222419971 | NA | 3.60E-06 | mr1140 | 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 |
| vg1222419971 | NA | 8.74E-07 | mr1613 | 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 |
| vg1222419971 | NA | 2.09E-06 | mr1962 | 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 |
| vg1222419971 | NA | 1.17E-07 | mr1057_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 |
| vg1222419971 | NA | 7.63E-07 | mr1071_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 |
| vg1222419971 | NA | 3.30E-06 | mr1080_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 |
| vg1222419971 | NA | 1.65E-07 | mr1100_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 |
| vg1222419971 | NA | 2.18E-09 | mr1126_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 |
| vg1222419971 | NA | 6.34E-08 | mr1203_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 |
| vg1222419971 | NA | 7.69E-08 | mr1613_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 |
| vg1222419971 | NA | 4.51E-06 | mr1691_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 |