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Detailed information for vg0430744499:

Variant ID: vg0430744499 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 30744499
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CCCGTTACGATGTGTATCTACAACCTCCCCCCTGGCTATGCATGAAGAGGAAGTACATAATGATGCCGATTATTATTCAAGGCCCCAAGCAACCTGGTAA[C/T]
AACATCGATGTGTACCTAAGACCACTGGTCGAAGATCTTAGGCTGTTGTGGAAGAAGGAAGGTGTCCCCGTGTGGGACGAGGATAAACAGGAGGAGTTTA

Reverse complement sequence

TAAACTCCTCCTGTTTATCCTCGTCCCACACGGGGACACCTTCCTTCTTCCACAACAGCCTAAGATCTTCGACCAGTGGTCTTAGGTACACATCGATGTT[G/A]
TTACCAGGTTGCTTGGGGCCTTGAATAATAATCGGCATCATTATGTACTTCCTCTTCATGCATAGCCAGGGGGGAGGTTGTAGATACACATCGTAACGGG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 78.80% 7.00% 1.35% 12.82% NA
All Indica  2759 76.90% 0.70% 1.70% 20.70% NA
All Japonica  1512 89.70% 9.20% 0.46% 0.66% NA
Aus  269 24.90% 63.60% 3.35% 8.18% NA
Indica I  595 74.30% 0.00% 1.68% 24.03% NA
Indica II  465 91.40% 0.20% 0.65% 7.74% NA
Indica III  913 72.10% 0.70% 1.75% 25.52% NA
Indica Intermediate  786 76.10% 1.40% 2.29% 20.23% NA
Temperate Japonica  767 98.30% 0.00% 0.78% 0.91% NA
Tropical Japonica  504 78.00% 21.60% 0.00% 0.40% NA
Japonica Intermediate  241 86.70% 12.40% 0.41% 0.41% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 91.10% 4.40% 1.11% 3.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0430744499 C -> DEL LOC_Os04g51840.1 N frameshift_variant Average:26.023; most accessible tissue: Minghui63 young leaf, score: 49.581 N N N N
vg0430744499 C -> T LOC_Os04g51840.1 synonymous_variant ; p.Asn48Asn; LOW synonymous_codon Average:26.023; most accessible tissue: Minghui63 young leaf, score: 49.581 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0430744499 NA 2.06E-07 mr1530 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
vg0430744499 3.77E-10 NA mr1745 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
vg0430744499 NA 3.79E-10 mr1047_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
vg0430744499 NA 1.93E-16 mr1530_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
vg0430744499 1.02E-11 NA mr1745_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
vg0430744499 2.75E-06 2.86E-06 mr1745_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
vg0430744499 NA 2.88E-08 mr1808_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
vg0430744499 NA 3.80E-06 mr1815_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