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Detailed information for vg1001981255:

Variant ID: vg1001981255 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 1981255
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTTAGATTTGATCTTAGAGAACGATTCTTTCGGCCGAAGCGAAGCCGTCCCGGAGGTCAAGATTATTTATGAAGATCCTCTGCACGAGGAGTTGGAACCC[A/G]
ACTCAACTGCCGAATCCTCATTCCGGTTGCTGGAGCCAGAGGAAGAGGAAATTCATCCTCCAGAAATTCCATTCCAATTCAAGGATGATCTTTATGAAGA

Reverse complement sequence

TCTTCATAAAGATCATCCTTGAATTGGAATGGAATTTCTGGAGGATGAATTTCCTCTTCCTCTGGCTCCAGCAACCGGAATGAGGATTCGGCAGTTGAGT[T/C]
GGGTTCCAACTCCTCGTGCAGAGGATCTTCATAAATAATCTTGACCTCCGGGACGGCTTCGCTTCGGCCGAAAGAATCGTTCTCTAAGATCAAATCTAAG

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 73.00% 14.70% 0.78% 11.45% NA
All Indica  2759 75.30% 7.90% 0.94% 15.91% NA
All Japonica  1512 70.00% 29.20% 0.26% 0.60% NA
Aus  269 58.00% 7.80% 1.49% 32.71% NA
Indica I  595 60.20% 22.20% 1.34% 16.30% NA
Indica II  465 81.30% 6.20% 0.86% 11.61% NA
Indica III  913 78.10% 0.80% 0.44% 20.70% NA
Indica Intermediate  786 79.90% 6.20% 1.27% 12.60% NA
Temperate Japonica  767 57.00% 42.20% 0.13% 0.65% NA
Tropical Japonica  504 95.40% 4.40% 0.00% 0.20% NA
Japonica Intermediate  241 58.10% 39.40% 1.24% 1.24% NA
VI/Aromatic  96 94.80% 3.10% 1.04% 1.04% NA
Intermediate  90 76.70% 16.70% 2.22% 4.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1001981255 A -> G LOC_Os10g04250.1 missense_variant ; p.Asn234Asp; MODERATE nonsynonymous_codon Average:23.26; most accessible tissue: Minghui63 flag leaf, score: 35.832 unknown unknown TOLERATED 1.00
vg1001981255 A -> DEL LOC_Os10g04250.1 N frameshift_variant Average:23.26; most accessible tissue: Minghui63 flag leaf, score: 35.832 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1001981255 7.34E-07 NA mr1679 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
vg1001981255 NA 5.04E-09 mr1691 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
vg1001981255 NA 3.42E-06 mr1691 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
vg1001981255 NA 3.77E-09 mr1693 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
vg1001981255 NA 2.28E-06 mr1748 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
vg1001981255 NA 4.45E-07 mr1768 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
vg1001981255 NA 5.89E-06 mr1768_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