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

Detailed information for vg0723457034:

Variant ID: vg0723457034 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 23457034
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATCAAACCGACGACCATCCATAATGGCATCAATAACATGCCAAGCAACTCCGCGTATGTCATCATTGTTGCCGCATCTTGGGAGGATGGTGGCCCTTACT[C/A]
TGCGGTTGATCACACTTGGGAGAGCCCTCAAACCCGCCACCTTTCCATATGTGTACCCTCCCCCTTCTTCATAAAACTGAGAAAAGTGATCAATGGGGAA

Reverse complement sequence

TTCCCCATTGATCACTTTTCTCAGTTTTATGAAGAAGGGGGAGGGTACACATATGGAAAGGTGGCGGGTTTGAGGGCTCTCCCAAGTGTGATCAACCGCA[G/T]
AGTAAGGGCCACCATCCTCCCAAGATGCGGCAACAATGATGACATACGCGGAGTTGCTTGGCATGTTATTGATGCCATTATGGATGGTCGTCGGTTTGAT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 24.20% 0.50% 7.36% 67.88% NA
All Indica  2759 5.50% 0.70% 7.29% 86.48% NA
All Japonica  1512 58.80% 0.10% 0.66% 40.41% NA
Aus  269 3.30% 1.10% 46.84% 48.70% NA
Indica I  595 5.40% 0.50% 2.69% 91.43% NA
Indica II  465 5.20% 0.00% 5.81% 89.03% NA
Indica III  913 3.30% 0.70% 9.20% 86.86% NA
Indica Intermediate  786 8.50% 1.30% 9.41% 80.79% NA
Temperate Japonica  767 86.40% 0.00% 0.13% 13.43% NA
Tropical Japonica  504 26.80% 0.40% 1.59% 71.23% NA
Japonica Intermediate  241 37.80% 0.00% 0.41% 61.83% NA
VI/Aromatic  96 62.50% 0.00% 2.08% 35.42% NA
Intermediate  90 37.80% 1.10% 10.00% 51.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0723457034 C -> DEL LOC_Os07g39150.1 N frameshift_variant Average:7.312; most accessible tissue: Callus, score: 14.641 N N N N
vg0723457034 C -> A LOC_Os07g39150.1 missense_variant ; p.Arg256Ile; MODERATE nonsynonymous_codon ; R256I Average:7.312; most accessible tissue: Callus, score: 14.641 probably damaging -2.21 TOLERATED 1.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0723457034 NA 2.06E-10 mr1471 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
vg0723457034 7.65E-13 9.99E-64 mr1563 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
vg0723457034 NA 3.23E-12 mr1563 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
vg0723457034 NA 7.20E-06 mr1654 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
vg0723457034 NA 4.13E-15 mr1933 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
vg0723457034 NA 8.41E-10 mr1093_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
vg0723457034 NA 6.23E-07 mr1248_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
vg0723457034 NA 1.01E-06 mr1257_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
vg0723457034 2.13E-17 3.91E-100 mr1563_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
vg0723457034 8.38E-07 5.21E-17 mr1563_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
vg0723457034 NA 3.23E-06 mr1827_2 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
vg0723457034 NA 1.62E-14 mr1902_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