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Detailed information for vg1121623328:

Variant ID: vg1121623328 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 21623328
Reference Allele: GAlternative Allele: A,C
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTGGAAATTGGCGACGAACTGTTGCCACAGGTCTGCCCACGAAGAGATTGAGTAGGGAGGAAGATGCATCAGCCATGAACGTGCAGAACCTTTCAACGCA[G/A,C]
TTGGTAAATAATTTGCCAACGCGTTGTCGTCTGCTCCGGCAGTGTAGAGTACTGTGGAGTAGACTTGAAGGAACTCCTCTGGGTCGGTGCTCCCATCATA

Reverse complement sequence

TATGATGGGAGCACCGACCCAGAGGAGTTCCTTCAAGTCTACTCCACAGTACTCTACACTGCCGGAGCAGACGACAACGCGTTGGCAAATTATTTACCAA[C/T,G]
TGCGTTGAAAGGTTCTGCACGTTCATGGCTGATGCATCTTCCTCCCTACTCAATCTCTTCGTGGGCAGACCTGTGGCAACAGTTCGTCGCCAATTTCCAA

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 88.10% 5.40% 4.95% 1.48% C: 0.04%
All Indica  2759 82.70% 9.00% 8.23% 0.04% C: 0.07%
All Japonica  1512 95.00% 0.30% 0.46% 4.30% NA
Aus  269 98.50% 0.40% 0.00% 1.12% NA
Indica I  595 78.80% 11.40% 9.58% 0.17% NA
Indica II  465 75.10% 14.40% 10.54% 0.00% NA
Indica III  913 90.00% 4.70% 5.04% 0.00% C: 0.22%
Indica Intermediate  786 81.60% 8.90% 9.54% 0.00% NA
Temperate Japonica  767 93.20% 0.40% 0.65% 5.74% NA
Tropical Japonica  504 98.80% 0.00% 0.20% 0.99% NA
Japonica Intermediate  241 92.50% 0.40% 0.41% 6.64% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 96.70% 2.20% 0.00% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1121623328 G -> A LOC_Os11g36640.1 missense_variant ; p.Thr476Ile; MODERATE nonsynonymous_codon ; T476I Average:9.191; most accessible tissue: Minghui63 flag leaf, score: 15.952 benign 1.271 DELETERIOUS 0.00
vg1121623328 G -> DEL LOC_Os11g36640.1 N frameshift_variant Average:9.191; most accessible tissue: Minghui63 flag leaf, score: 15.952 N N N N
vg1121623328 G -> C LOC_Os11g36640.1 missense_variant ; p.Thr476Ser; MODERATE nonsynonymous_codon ; T476S Average:9.191; most accessible tissue: Minghui63 flag leaf, score: 15.952 benign 0.289 TOLERATED 0.11

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1121623328 2.50E-06 NA mr1412 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
vg1121623328 3.05E-06 3.06E-06 mr1412 Ind_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