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Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0319794993:

Variant ID: vg0319794993 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 19794993
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GATTAGAGCCGACTGTTAACGATGACGGAGAGGAACTCACTCATCGGAGATTCACATCATATGGAGAGTACGCCTCTACCCCAACTGCTGCAGGAGCAAA[A/G]
CTATCGGCCGAGCTGCTCAAAGATTGGTTTTGTAGCTTTTATGAGGGGTTCCAAAAGGATGCTCGAGCTTGGTTTCTCTATGGAGACTCAACACTTCTGG

Reverse complement sequence

CCAGAAGTGTTGAGTCTCCATAGAGAAACCAAGCTCGAGCATCCTTTTGGAACCCCTCATAAAAGCTACAAAACCAATCTTTGAGCAGCTCGGCCGATAG[T/C]
TTTGCTCCTGCAGCAGTTGGGGTAGAGGCGTACTCTCCATATGATGTGAATCTCCGATGAGTGAGTTCCTCTCCGTCATCGTTAACAGTCGGCTCTAATC

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 61.40% 11.20% 26.98% 0.36% NA
All Indica  2759 46.70% 12.40% 40.92% 0.00% NA
All Japonica  1512 87.50% 10.20% 1.19% 1.12% NA
Aus  269 59.10% 8.20% 32.71% 0.00% NA
Indica I  595 42.70% 6.90% 50.42% 0.00% NA
Indica II  465 38.30% 12.50% 49.25% 0.00% NA
Indica III  913 55.50% 13.70% 30.78% 0.00% NA
Indica Intermediate  786 44.40% 15.00% 40.59% 0.00% NA
Temperate Japonica  767 99.90% 0.00% 0.13% 0.00% NA
Tropical Japonica  504 68.70% 27.60% 2.78% 0.99% NA
Japonica Intermediate  241 87.60% 6.20% 1.24% 4.98% NA
VI/Aromatic  96 79.20% 5.20% 15.62% 0.00% NA
Intermediate  90 64.40% 7.80% 27.78% 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
vg0319794993 A -> DEL LOC_Os03g35730.1 N frameshift_variant Average:38.825; most accessible tissue: Zhenshan97 flag leaf, score: 56.722 N N N N
vg0319794993 A -> G LOC_Os03g35730.1 synonymous_variant ; p.Lys189Lys; LOW synonymous_codon Average:38.825; most accessible tissue: Zhenshan97 flag leaf, score: 56.722 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0319794993 NA 5.05E-10 mr1217 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
vg0319794993 NA 3.62E-06 mr1227 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
vg0319794993 NA 4.86E-06 mr1350 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
vg0319794993 NA 1.88E-06 mr1583 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
vg0319794993 NA 2.55E-06 mr1622 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
vg0319794993 NA 3.27E-07 mr1750 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
vg0319794993 NA 1.53E-08 mr1827 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
vg0319794993 NA 1.81E-09 mr1845 Jap_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
vg0319794993 NA 1.44E-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
vg0319794993 NA 2.21E-09 mr1852 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
vg0319794993 NA 3.42E-08 mr1136_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