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Detailed information for vg1009605363:

Variant ID: vg1009605363 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 9605363
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GAGCGGCCGGTTCCGTTCGCCAGTTTCGGTCGATCATTTCGGTGATCCCGTGTCACGTTAAATTGACTCGTTGAGTCGGTATCTCGTGAGGTTTGCTTGC[T/C]
AGTCAACCTATCCTTTGATCCTATGTTCCTTTTGGGCTCTAATTCCTATCAATTGATTAAGTTTCTGTCAATAGTAAATAACACAGAGCATCTTGTAAAA

Reverse complement sequence

TTTTACAAGATGCTCTGTGTTATTTACTATTGACAGAAACTTAATCAATTGATAGGAATTAGAGCCCAAAAGGAACATAGGATCAAAGGATAGGTTGACT[A/G]
GCAAGCAAACCTCACGAGATACCGACTCAACGAGTCAATTTAACGTGACACGGGATCACCGAAATGATCGACCGAAACTGGCGAACGGAACCGGCCGCTC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 86.60% 12.90% 0.47% 0.00% NA
All Indica  2759 98.90% 1.00% 0.04% 0.00% NA
All Japonica  1512 61.00% 37.60% 1.32% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.20% 0.70% 0.17% 0.00% NA
Indica II  465 99.40% 0.60% 0.00% 0.00% NA
Indica III  913 99.20% 0.80% 0.00% 0.00% NA
Indica Intermediate  786 98.20% 1.80% 0.00% 0.00% NA
Temperate Japonica  767 38.70% 58.80% 2.48% 0.00% NA
Tropical Japonica  504 92.70% 7.10% 0.20% 0.00% NA
Japonica Intermediate  241 66.00% 34.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 83.30% 15.60% 1.11% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1009605363 T -> C LOC_Os10g18850.1 downstream_gene_variant ; 1849.0bp to feature; MODIFIER silent_mutation Average:33.934; most accessible tissue: Zhenshan97 flag leaf, score: 49.013 N N N N
vg1009605363 T -> C LOC_Os10g18840-LOC_Os10g18850 intergenic_region ; MODIFIER silent_mutation Average:33.934; most accessible tissue: Zhenshan97 flag leaf, score: 49.013 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1009605363 NA 3.18E-06 mr1094_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
vg1009605363 NA 7.14E-07 mr1250_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
vg1009605363 NA 3.88E-07 mr1570_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
vg1009605363 5.37E-06 NA mr1617_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
vg1009605363 NA 8.23E-07 mr1617_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
vg1009605363 9.45E-07 NA mr1648_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
vg1009605363 NA 1.49E-17 mr1682_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
vg1009605363 NA 6.47E-07 mr1682_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
vg1009605363 NA 2.16E-06 mr1763_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