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Detailed information for vg1004450805:

Variant ID: vg1004450805 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 4450805
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGACGAAGCCTACTCCTCGGAAAAGTCACCATCCGACGCATACTCAAACTCTGGGGTTTTGGGGAAAATAGAGCAAGACTGAGTACAACCACCGTACTCA[G/A]
CAAGTCATACCGGAACAGGGGGTATGATGCAGGATATAACCAAAGGATAGCTAAAGCGGTTCATTTGCATAAATTGAGCATTTATAAACAGTAGTTGAAA

Reverse complement sequence

TTTCAACTACTGTTTATAAATGCTCAATTTATGCAAATGAACCGCTTTAGCTATCCTTTGGTTATATCCTGCATCATACCCCCTGTTCCGGTATGACTTG[C/T]
TGAGTACGGTGGTTGTACTCAGTCTTGCTCTATTTTCCCCAAAACCCCAGAGTTTGAGTATGCGTCGGATGGTGACTTTTCCGAGGAGTAGGCTTCGTCC

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 71.60% 9.60% 0.85% 17.92% NA
All Indica  2759 83.00% 0.70% 1.09% 15.22% NA
All Japonica  1512 62.00% 26.10% 0.20% 11.64% NA
Aus  269 16.00% 0.00% 1.49% 82.53% NA
Indica I  595 65.70% 0.00% 1.68% 32.61% NA
Indica II  465 82.60% 0.20% 0.86% 16.34% NA
Indica III  913 91.50% 0.80% 1.31% 6.46% NA
Indica Intermediate  786 86.50% 1.40% 0.51% 11.58% NA
Temperate Japonica  767 89.20% 5.50% 0.00% 5.35% NA
Tropical Japonica  504 26.80% 59.50% 0.40% 13.29% NA
Japonica Intermediate  241 49.40% 22.00% 0.41% 28.22% NA
VI/Aromatic  96 50.00% 26.00% 3.12% 20.83% NA
Intermediate  90 74.40% 15.60% 0.00% 10.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1004450805 G -> A LOC_Os10g08230.1 downstream_gene_variant ; 3509.0bp to feature; MODIFIER silent_mutation Average:18.454; most accessible tissue: Callus, score: 30.618 N N N N
vg1004450805 G -> A LOC_Os10g08240.1 intron_variant ; MODIFIER silent_mutation Average:18.454; most accessible tissue: Callus, score: 30.618 N N N N
vg1004450805 G -> DEL N N silent_mutation Average:18.454; most accessible tissue: Callus, score: 30.618 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1004450805 4.71E-06 NA 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
vg1004450805 NA 5.73E-07 mr1248 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
vg1004450805 NA 6.99E-09 mr1248 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
vg1004450805 2.10E-06 NA mr1471 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
vg1004450805 NA 1.25E-08 mr1471 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
vg1004450805 1.08E-07 NA mr1477 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
vg1004450805 NA 1.15E-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
vg1004450805 NA 3.77E-10 mr1642 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
vg1004450805 NA 1.10E-06 mr1642 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
vg1004450805 NA 4.41E-06 mr1782 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
vg1004450805 NA 9.53E-07 mr1797 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
vg1004450805 NA 9.53E-07 mr1801 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
vg1004450805 NA 8.54E-07 mr1553_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
vg1004450805 NA 1.16E-06 mr1632_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
vg1004450805 NA 4.21E-07 mr1696_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
vg1004450805 NA 6.21E-08 mr1817_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