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Detailed information for vg1000735141:

Variant ID: vg1000735141 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 735141
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 218. )

Flanking Sequence (100 bp) in Reference Genome:


CACCGCTTGTCTGTACCCCTTAACCAATCGCGTTTTTTAAAACTTTTCGTTGGTTCCGACTGCCTTTGTGTGTGCAATCATCACCTTAGTTTTCTTTGGC[G/A]
TTTTGATTCCGGGTAATTAGTTTGTTGTTTGTAGAGATGTCGATGTCGAGGATATCCAGCAGCGCGGGCAGCCTGAATTGCCGGTAGTCGTTCCAGCACT

Reverse complement sequence

AGTGCTGGAACGACTACCGGCAATTCAGGCTGCCCGCGCTGCTGGATATCCTCGACATCGACATCTCTACAAACAACAAACTAATTACCCGGAATCAAAA[C/T]
GCCAAAGAAAACTAAGGTGATGATTGCACACACAAAGGCAGTCGGAACCAACGAAAAGTTTTAAAAAACGCGATTGGTTAAGGGGTACAGACAAGCGGTG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 59.90% 2.90% 11.13% 26.13% NA
All Indica  2759 55.70% 2.00% 8.92% 33.38% NA
All Japonica  1512 57.90% 5.00% 17.59% 19.58% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 67.60% 0.70% 3.70% 28.07% NA
Indica II  465 28.20% 2.40% 12.90% 56.56% NA
Indica III  913 56.30% 2.60% 11.50% 29.57% NA
Indica Intermediate  786 62.30% 2.00% 7.51% 28.12% NA
Temperate Japonica  767 88.40% 1.00% 4.04% 6.52% NA
Tropical Japonica  504 10.70% 12.10% 38.49% 38.69% NA
Japonica Intermediate  241 59.30% 2.50% 17.01% 21.16% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 61.10% 3.30% 15.56% 20.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1000735141 G -> A LOC_Os10g02160.1 downstream_gene_variant ; 1511.0bp to feature; MODIFIER silent_mutation Average:26.853; most accessible tissue: Zhenshan97 flag leaf, score: 76.925 N N N N
vg1000735141 G -> A LOC_Os10g02170.1 downstream_gene_variant ; 4516.0bp to feature; MODIFIER silent_mutation Average:26.853; most accessible tissue: Zhenshan97 flag leaf, score: 76.925 N N N N
vg1000735141 G -> A LOC_Os10g02150.1 intron_variant ; MODIFIER silent_mutation Average:26.853; most accessible tissue: Zhenshan97 flag leaf, score: 76.925 N N N N
vg1000735141 G -> DEL N N silent_mutation Average:26.853; most accessible tissue: Zhenshan97 flag leaf, score: 76.925 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1000735141 NA 1.64E-08 mr1090 Ind_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
vg1000735141 NA 1.15E-09 mr1211 Ind_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
vg1000735141 8.00E-06 NA mr1536 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
vg1000735141 1.88E-06 1.03E-09 mr1539 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
vg1000735141 NA 3.50E-06 mr1906 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
vg1000735141 NA 9.71E-08 mr1090_2 Ind_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
vg1000735141 NA 2.56E-09 mr1211_2 Ind_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