Variant ID: vg0723469618 (JBrowse) | Variation Type: SNP |
Chromosome: chr07 | Position: 23469618 |
Reference Allele: G | Alternative Allele: A |
Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GTTGTAGCCCTGTCAGAGGGCCCCATCGGCCTGGCCGGTCAGACCGCCATCGGCTCGGTCTGACCGACTACAGCTCGGTCGGCTCTGTATCGGCCATCCC[G/A]
AGCAGCATCGTCTCGGCCTCCAAGAGGCCGGTCTGACCGGGAAAGTGCCTCCGGTCAGACCGCCACTATGTAGCCGGTCTGACCGGCCAGGGCACGCCGA
TCGGCGTGCCCTGGCCGGTCAGACCGGCTACATAGTGGCGGTCTGACCGGAGGCACTTTCCCGGTCAGACCGGCCTCTTGGAGGCCGAGACGATGCTGCT[C/T]
GGGATGGCCGATACAGAGCCGACCGAGCTGTAGTCGGTCAGACCGAGCCGATGGCGGTCTGACCGGCCAGGCCGATGGGGCCCTCTGACAGGGCTACAAC
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 | 81.40% | 16.30% | 0.34% | 2.01% | NA |
All Indica | 2759 | 91.30% | 7.60% | 0.40% | 0.72% | NA |
All Japonica | 1512 | 62.00% | 33.10% | 0.33% | 4.63% | NA |
Aus | 269 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
Indica I | 595 | 98.80% | 1.20% | 0.00% | 0.00% | NA |
Indica II | 465 | 90.30% | 5.40% | 0.86% | 3.44% | NA |
Indica III | 913 | 87.60% | 11.80% | 0.55% | 0.00% | NA |
Indica Intermediate | 786 | 90.50% | 8.80% | 0.25% | 0.51% | NA |
Temperate Japonica | 767 | 86.80% | 12.90% | 0.26% | 0.00% | NA |
Tropical Japonica | 504 | 28.80% | 59.90% | 0.20% | 11.11% | NA |
Japonica Intermediate | 241 | 52.30% | 41.10% | 0.83% | 5.81% | NA |
VI/Aromatic | 96 | 64.60% | 35.40% | 0.00% | 0.00% | NA |
Intermediate | 90 | 67.80% | 26.70% | 0.00% | 5.56% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0723469618 | G -> DEL | N | N | silent_mutation | Average:15.828; most accessible tissue: Minghui63 young leaf, score: 23.613 | N | N | N | N |
vg0723469618 | G -> A | LOC_Os07g39170.1 | upstream_gene_variant ; 1076.0bp to feature; MODIFIER | silent_mutation | Average:15.828; most accessible tissue: Minghui63 young leaf, score: 23.613 | N | N | N | N |
vg0723469618 | G -> A | LOC_Os07g39180.1 | downstream_gene_variant ; 1710.0bp to feature; MODIFIER | silent_mutation | Average:15.828; most accessible tissue: Minghui63 young leaf, score: 23.613 | N | N | N | N |
vg0723469618 | G -> A | LOC_Os07g39170-LOC_Os07g39180 | intergenic_region ; MODIFIER | silent_mutation | Average:15.828; most accessible tissue: Minghui63 young leaf, score: 23.613 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0723469618 | 4.16E-15 | NA | mr1563 | 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 |
vg0723469618 | 1.93E-12 | 2.59E-21 | mr1563 | 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 |
vg0723469618 | 1.70E-18 | NA | mr1563_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 |
vg0723469618 | 8.33E-16 | 4.11E-25 | mr1563_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 |