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Detailed information for vg1004573441:

Variant ID: vg1004573441 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 4573441
Reference Allele: AAlternative Allele: C
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.74, A: 0.26, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:


GACTAGTCCGATACTTTGAGGATGGGAAACGAAGCGAAGCATATTTTGACTCCCAGCCCGATGCAGTAATCCTGGAAATCGGTGCTGATGAACTGGGAGC[A/C]
GTTGTCAGTAATGATGCGATGCGGTAGTCCGTATCTGCAAAATATTCCCTTGATGAACTTGATGGCGTTGGCGGCTTTGATTTCCCCCGTGGGAACTGCT

Reverse complement sequence

AGCAGTTCCCACGGGGGAAATCAAAGCCGCCAACGCCATCAAGTTCATCAAGGGAATATTTTGCAGATACGGACTACCGCATCGCATCATTACTGACAAC[T/G]
GCTCCCAGTTCATCAGCACCGATTTCCAGGATTACTGCATCGGGCTGGGAGTCAAAATATGCTTCGCTTCGTTTCCCATCCTCAAAGTATCGGACTAGTC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 47.90% 25.10% 1.40% 25.62% NA
All Indica  2759 48.40% 21.10% 1.45% 29.10% NA
All Japonica  1512 56.70% 17.60% 1.59% 24.14% NA
Aus  269 3.70% 95.50% 0.00% 0.74% NA
Indica I  595 40.80% 41.20% 0.34% 17.65% NA
Indica II  465 62.20% 16.30% 2.80% 18.71% NA
Indica III  913 51.90% 13.50% 0.77% 33.84% NA
Indica Intermediate  786 41.70% 17.60% 2.29% 38.42% NA
Temperate Japonica  767 77.20% 17.60% 0.39% 4.82% NA
Tropical Japonica  504 18.80% 22.60% 3.77% 54.76% NA
Japonica Intermediate  241 70.50% 7.10% 0.83% 21.58% NA
VI/Aromatic  96 16.70% 57.30% 0.00% 26.04% NA
Intermediate  90 51.10% 28.90% 2.22% 17.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1004573441 A -> C LOC_Os10g08420.1 missense_variant ; p.Cys344Gly; MODERATE nonsynonymous_codon ; C344G Average:53.256; most accessible tissue: Zhenshan97 flag leaf, score: 77.203 benign -1.198 TOLERATED 1.00
vg1004573441 A -> DEL LOC_Os10g08420.1 N frameshift_variant Average:53.256; most accessible tissue: Zhenshan97 flag leaf, score: 77.203 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1004573441 NA 3.88E-07 mr1808 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
vg1004573441 6.20E-06 NA mr1853 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
vg1004573441 3.30E-06 NA mr1053_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
vg1004573441 NA 9.06E-06 mr1308_2 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
vg1004573441 2.46E-06 2.43E-06 mr1318_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
vg1004573441 NA 1.27E-07 mr1379_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
vg1004573441 NA 4.58E-07 mr1401_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
vg1004573441 NA 4.34E-06 mr1415_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
vg1004573441 NA 1.79E-08 mr1471_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
vg1004573441 NA 9.52E-08 mr1559_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
vg1004573441 NA 4.24E-07 mr1606_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
vg1004573441 NA 2.52E-08 mr1642_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
vg1004573441 NA 2.13E-07 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
vg1004573441 1.78E-06 NA mr1853_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
vg1004573441 NA 1.06E-06 mr1888_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
vg1004573441 5.06E-06 NA mr1897_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
vg1004573441 NA 1.97E-13 mr1942_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