| Variant ID: vg0715326471 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr07 | Position: 15326471 |
| Reference Allele: C | Alternative Allele: CCTCTAATAGAGGACACCTTTATAT,CTTCTAATAGAGGACACCTTATATGAAACGATTCATTTATAACCAGCTTATAT,CCTCTAATAGAGGACACCTTATATGAAACGATTCATTTATAACCAGCTTATAT,T,CTTCTAATAGAGGACACCTTATAT,CTTCTAATAGAG |
| Primary Allele: C | Secondary Allele: CTTCTAATAGAGGACACCTT ATATGAAACGATTCATTTAT AACCAGCTTATAT |
Inferred Ancestral Allele: Not determined.
TATATAGAAAACCTTTTTAGAAAAAGAGTATCATTCACTACTACAAAACCTCTAATAGGGGACACCTTATATGAACCGATTCATTTAGAACCAGCTTATA[C/CCTCTAATAGAGGACACCTTTATAT,CTTCTAATAGAGGACACCTTATATGAAACGATTCATTTATAACCAGCTTATAT,CCTCTAATAGAGGACACCTTATATGAAACGATTCATTTATAACCAGCTTATAT,T,CTTCTAATAGAGGACACCTTATAT,CTTCTAATAGAG]
GAAGCTTTTCCCGTCCATCCAACACCACACATAAGGCTAAAAAAACTAGCACCAATAAGTATCATATGTGATGGTTCTTATTAAAAGCCGGTACATATAA
TTATATGTACCGGCTTTTAATAAGAACCATCACATATGATACTTATTGGTGCTAGTTTTTTTAGCCTTATGTGTGGTGTTGGATGGACGGGAAAAGCTTC[G/ATATAAAGGTGTCCTCTATTAGAGG,ATATAAGCTGGTTATAAATGAATCGTTTCATATAAGGTGTCCTCTATTAGAAG,ATATAAGCTGGTTATAAATGAATCGTTTCATATAAGGTGTCCTCTATTAGAGG,A,ATATAAGGTGTCCTCTATTAGAAG,CTCTATTAGAAG]
TATAAGCTGGTTCTAAATGAATCGGTTCATATAAGGTGTCCCCTATTAGAGGTTTTGTAGTAGTGAATGATACTCTTTTTCTAAAAAGGTTTTCTATATA
| Populations | Population Size | Frequency of C(primary allele) | Frequency of CTTCTAATAGAGGACACCTT ATATGAAACGATTCATTTAT AACCAGCTTATAT(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 38.50% | 35.90% | 5.56% | 4.42% | CCTCTAATAGAGGACACCTTATATGAAACGATTCATTTATAACCAGCTTATAT: 6.81%; CCTCTAATAGAGGACACCTTTATAT: 5.27%; T: 3.28%; CTTCTAATAGAGGACACCTTATAT: 0.21%; CTTCTAATAGAG: 0.08% |
| All Indica | 2759 | 6.00% | 58.60% | 3.55% | 6.16% | CCTCTAATAGAGGACACCTTATATGAAACGATTCATTTATAACCAGCTTATAT: 11.56%; CCTCTAATAGAGGACACCTTTATAT: 8.77%; T: 4.86%; CTTCTAATAGAGGACACCTTATAT: 0.33%; CTTCTAATAGAG: 0.14% |
| All Japonica | 1512 | 99.10% | 0.80% | 0.07% | 0.00% | CCTCTAATAGAGGACACCTTTATAT: 0.07% |
| Aus | 269 | 9.30% | 12.30% | 58.74% | 13.01% | T: 5.58%; CCTCTAATAGAGGACACCTTTATAT: 0.74%; CCTCTAATAGAGGACACCTTATATGAAACGATTCATTTATAACCAGCTTATAT: 0.37% |
| Indica I | 595 | 2.20% | 52.80% | 4.87% | 4.20% | CCTCTAATAGAGGACACCTTATATGAAACGATTCATTTATAACCAGCTTATAT: 23.36%; CCTCTAATAGAGGACACCTTTATAT: 8.57%; T: 3.70%; CTTCTAATAGAGGACACCTTATAT: 0.34% |
| Indica II | 465 | 4.50% | 76.60% | 3.44% | 0.65% | T: 6.45%; CCTCTAATAGAGGACACCTTATATGAAACGATTCATTTATAACCAGCTTATAT: 6.24%; CCTCTAATAGAGGACACCTTTATAT: 1.72%; CTTCTAATAGAGGACACCTTATAT: 0.43% |
| Indica III | 913 | 1.90% | 63.10% | 1.10% | 8.87% | CCTCTAATAGAGGACACCTTTATAT: 11.06%; CCTCTAATAGAGGACACCTTATATGAAACGATTCATTTATAACCAGCTTATAT: 8.32%; T: 4.93%; CTTCTAATAGAG: 0.44%; CTTCTAATAGAGGACACCTTATAT: 0.33% |
| Indica Intermediate | 786 | 14.60% | 47.20% | 5.47% | 7.76% | CCTCTAATAGAGGACACCTTTATAT: 10.43%; CCTCTAATAGAGGACACCTTATATGAAACGATTCATTTATAACCAGCTTATAT: 9.54%; T: 4.71%; CTTCTAATAGAGGACACCTTATAT: 0.25% |
| Temperate Japonica | 767 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.40% | 0.40% | 0.00% | 0.00% | CCTCTAATAGAGGACACCTTTATAT: 0.20% |
| Japonica Intermediate | 241 | 98.80% | 0.80% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 87.50% | 12.50% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 50.00% | 24.40% | 6.67% | 4.44% | T: 6.67%; CCTCTAATAGAGGACACCTTTATAT: 4.44%; CCTCTAATAGAGGACACCTTATATGAAACGATTCATTTATAACCAGCTTATAT: 2.22%; CTTCTAATAGAGGACACCTTATAT: 1.11% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0715326471 | C -> CTTCTAATAGAG | LOC_Os07g26600.1 | upstream_gene_variant ; 3375.0bp to feature; MODIFIER | silent_mutation | Average:36.932; most accessible tissue: Callus, score: 93.804 | N | N | N | N |
| vg0715326471 | C -> CTTCTAATAGAG | LOC_Os07g26600-LOC_Os07g26610 | intergenic_region ; MODIFIER | silent_mutation | Average:36.932; most accessible tissue: Callus, score: 93.804 | N | N | N | N |
| vg0715326471 | C -> T | LOC_Os07g26600.1 | upstream_gene_variant ; 3374.0bp to feature; MODIFIER | silent_mutation | Average:36.932; most accessible tissue: Callus, score: 93.804 | N | N | N | N |
| vg0715326471 | C -> T | LOC_Os07g26600-LOC_Os07g26610 | intergenic_region ; MODIFIER | silent_mutation | Average:36.932; most accessible tissue: Callus, score: 93.804 | N | N | N | N |
| vg0715326471 | C -> CTTCTAATAGAGGACACCTTATATGAAACG ATTCATTTATAACCAGCTTATAT | LOC_Os07g26600.1 | upstream_gene_variant ; 3375.0bp to feature; MODIFIER | silent_mutation | Average:36.932; most accessible tissue: Callus, score: 93.804 | N | N | N | N |
| vg0715326471 | C -> CTTCTAATAGAGGACACCTTATATGAAACG ATTCATTTATAACCAGCTTATAT | LOC_Os07g26600-LOC_Os07g26610 | intergenic_region ; MODIFIER | silent_mutation | Average:36.932; most accessible tissue: Callus, score: 93.804 | N | N | N | N |
| vg0715326471 | C -> CTTCTAATAGAGGACACCTTATAT | LOC_Os07g26600.1 | upstream_gene_variant ; 3375.0bp to feature; MODIFIER | silent_mutation | Average:36.932; most accessible tissue: Callus, score: 93.804 | N | N | N | N |
| vg0715326471 | C -> CTTCTAATAGAGGACACCTTATAT | LOC_Os07g26600-LOC_Os07g26610 | intergenic_region ; MODIFIER | silent_mutation | Average:36.932; most accessible tissue: Callus, score: 93.804 | N | N | N | N |
| vg0715326471 | C -> DEL | N | N | silent_mutation | Average:36.932; most accessible tissue: Callus, score: 93.804 | N | N | N | N |
| vg0715326471 | C -> CCTCTAATAGAGGACACCTTATATGAAACG ATTCATTTATAACCAGCTTATAT | LOC_Os07g26600.1 | upstream_gene_variant ; 3375.0bp to feature; MODIFIER | silent_mutation | Average:36.932; most accessible tissue: Callus, score: 93.804 | N | N | N | N |
| vg0715326471 | C -> CCTCTAATAGAGGACACCTTATATGAAACG ATTCATTTATAACCAGCTTATAT | LOC_Os07g26600-LOC_Os07g26610 | intergenic_region ; MODIFIER | silent_mutation | Average:36.932; most accessible tissue: Callus, score: 93.804 | N | N | N | N |
| vg0715326471 | C -> CCTCTAATAGAGGACACCTTTATAT | LOC_Os07g26600.1 | upstream_gene_variant ; 3375.0bp to feature; MODIFIER | silent_mutation | Average:36.932; most accessible tissue: Callus, score: 93.804 | N | N | N | N |
| vg0715326471 | C -> CCTCTAATAGAGGACACCTTTATAT | LOC_Os07g26600-LOC_Os07g26610 | intergenic_region ; MODIFIER | silent_mutation | Average:36.932; most accessible tissue: Callus, score: 93.804 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0715326471 | NA | 3.56E-21 | mr1155 | 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 |
| vg0715326471 | NA | 4.68E-12 | mr1281 | 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 |
| vg0715326471 | NA | 9.13E-07 | mr1510 | 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 |
| vg0715326471 | NA | 8.40E-26 | mr1537 | 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 |
| vg0715326471 | NA | 1.11E-17 | mr1566 | 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 |
| vg0715326471 | NA | 7.58E-58 | mr1594 | 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 |
| vg0715326471 | NA | 1.69E-11 | mr1630 | 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 |
| vg0715326471 | NA | 3.89E-52 | mr1795 | 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 |
| vg0715326471 | NA | 1.08E-25 | mr1888 | 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 |
| vg0715326471 | NA | 5.78E-39 | mr1890 | 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 |
| vg0715326471 | NA | 5.39E-40 | mr1891 | 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 |
| vg0715326471 | NA | 1.09E-07 | mr1915 | 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 |
| vg0715326471 | NA | 1.09E-07 | mr1335_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 |