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Detailed information for vg0921835488:

Variant ID: vg0921835488 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 21835488
Reference Allele: GAlternative Allele: C
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGGGGCGAAGGGAGTACTCCGTTTCCTATGACTATGGATGGGATGTCCAAATTGTTGAAGATGGTGTGTTGGGCGACTTCGGTCATCATCTTCTTTGCGG[G/C]
CATGCTCAGCTGCAAGTGCAACCATGGAAGCTCGGAGAAATCGCTTCTGGCTACCTCCCCAATCGAAACGCCTGATATTGAAAATTCTGCTCCAACTGCT

Reverse complement sequence

AGCAGTTGGAGCAGAATTTTCAATATCAGGCGTTTCGATTGGGGAGGTAGCCAGAAGCGATTTCTCCGAGCTTCCATGGTTGCACTTGCAGCTGAGCATG[C/G]
CCGCAAAGAAGATGATGACCGAAGTCGCCCAACACACCATCTTCAACAATTTGGACATCCCATCCATAGTCATAGGAAACGGAGTACTCCCTTCGCCCCA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 62.00% 35.10% 0.78% 2.16% NA
All Indica  2759 96.40% 1.40% 0.54% 1.70% NA
All Japonica  1512 1.70% 98.30% 0.00% 0.00% NA
Aus  269 70.30% 1.90% 7.81% 20.07% NA
Indica I  595 90.80% 1.00% 1.85% 6.39% NA
Indica II  465 97.00% 2.60% 0.43% 0.00% NA
Indica III  913 99.50% 0.30% 0.11% 0.11% NA
Indica Intermediate  786 96.70% 2.20% 0.13% 1.02% NA
Temperate Japonica  767 0.50% 99.50% 0.00% 0.00% NA
Tropical Japonica  504 3.80% 96.20% 0.00% 0.00% NA
Japonica Intermediate  241 1.20% 98.80% 0.00% 0.00% NA
VI/Aromatic  96 16.70% 83.30% 0.00% 0.00% NA
Intermediate  90 43.30% 54.40% 1.11% 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
vg0921835488 G -> DEL LOC_Os09g37870.1 N frameshift_variant Average:47.384; most accessible tissue: Zhenshan97 flower, score: 78.132 N N N N
vg0921835488 G -> C LOC_Os09g37870.1 missense_variant ; p.Gly359Ala; MODERATE nonsynonymous_codon ; G359A Average:47.384; most accessible tissue: Zhenshan97 flower, score: 78.132 unknown unknown TOLERATED 1.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0921835488 NA 1.09E-26 mr1024 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
vg0921835488 5.04E-06 NA mr1098 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
vg0921835488 NA 2.84E-28 mr1148 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
vg0921835488 NA 2.21E-15 mr1228 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
vg0921835488 NA 2.11E-15 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
vg0921835488 NA 4.94E-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
vg0921835488 NA 8.88E-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
vg0921835488 NA 8.51E-16 mr1361 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
vg0921835488 NA 4.47E-14 mr1376 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
vg0921835488 NA 4.47E-14 mr1431 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
vg0921835488 NA 1.51E-40 mr1509 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
vg0921835488 NA 7.16E-09 mr1575 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
vg0921835488 3.90E-06 NA mr1603 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
vg0921835488 NA 3.08E-07 mr1659 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
vg0921835488 NA 5.50E-06 mr1681 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
vg0921835488 NA 1.80E-08 mr1776 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
vg0921835488 NA 1.94E-06 mr1850 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
vg0921835488 NA 3.74E-12 mr1940 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
vg0921835488 NA 7.78E-23 mr1386_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