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Detailed information for vg1000966667:

Variant ID: vg1000966667 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 966667
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGCTAAGACCTGCAAGAGATAATATTGTGGATGGTTAAGGATCAAAACATGATTGGCCGATCTCAGATTTGTATCAACAAAAACTTACTGGAATAGCAGG[G/A]
GCAGCTGGTTGTTCTTCCTCTTCGACGTTGTGGCTGTCTGCAGCCGATGGAGTACGGTTGCCTGATTCTAGCTGCACAGGAGGTGAAGGAGGACGAGGAG

Reverse complement sequence

CTCCTCGTCCTCCTTCACCTCCTGTGCAGCTAGAATCAGGCAACCGTACTCCATCGGCTGCAGACAGCCACAACGTCGAAGAGGAAGAACAACCAGCTGC[C/T]
CCTGCTATTCCAGTAAGTTTTTGTTGATACAAATCTGAGATCGGCCAATCATGTTTTGATCCTTAACCATCCACAATATTATCTCTTGCAGGTCTTAGCC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 60.80% 33.90% 3.79% 1.50% NA
All Indica  2759 92.20% 3.10% 3.95% 0.72% NA
All Japonica  1512 3.80% 89.90% 2.91% 3.31% NA
Aus  269 85.50% 6.30% 8.18% 0.00% NA
Indica I  595 92.40% 3.50% 3.53% 0.50% NA
Indica II  465 93.80% 2.80% 2.58% 0.86% NA
Indica III  913 93.40% 1.90% 4.27% 0.44% NA
Indica Intermediate  786 89.80% 4.30% 4.71% 1.15% NA
Temperate Japonica  767 1.30% 97.70% 0.39% 0.65% NA
Tropical Japonica  504 4.00% 82.10% 7.94% 5.95% NA
Japonica Intermediate  241 11.60% 81.70% 0.41% 6.22% NA
VI/Aromatic  96 9.40% 89.60% 1.04% 0.00% NA
Intermediate  90 36.70% 58.90% 3.33% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1000966667 G -> A LOC_Os10g02560.1 synonymous_variant ; p.Ala566Ala; LOW synonymous_codon Average:25.191; most accessible tissue: Zhenshan97 young leaf, score: 34.553 N N N N
vg1000966667 G -> DEL LOC_Os10g02560.1 N frameshift_variant Average:25.191; most accessible tissue: Zhenshan97 young leaf, score: 34.553 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1000966667 NA 1.48E-19 mr1021 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
vg1000966667 NA 1.03E-09 mr1322 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
vg1000966667 NA 1.13E-16 mr1323 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
vg1000966667 NA 1.75E-15 mr1324 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
vg1000966667 NA 1.58E-11 mr1325 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
vg1000966667 NA 2.07E-13 mr1326 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
vg1000966667 NA 8.36E-13 mr1335 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
vg1000966667 NA 7.13E-86 mr1504 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
vg1000966667 NA 1.01E-06 mr1527 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
vg1000966667 NA 1.48E-12 mr1553 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
vg1000966667 NA 5.09E-12 mr1623 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
vg1000966667 NA 1.96E-07 mr1690 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
vg1000966667 NA 7.39E-22 mr1698 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
vg1000966667 5.53E-07 NA mr1172_2 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
vg1000966667 NA 2.44E-12 mr1553_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
vg1000966667 NA 4.08E-10 mr1756_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