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Detailed information for vg0112723651:

Variant ID: vg0112723651 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 12723651
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCGGCGGCGACGGAGGCAGGCCGGCGGTGTAGATGACGATGCCCATCAACGGTGGTGTGACCAACCGACCGTGTAGGCGGGGACACCAGTCGGCGGCGAC[A/G]
GAGGCAGGCCGGCGGTGAAGTCGTAGACGCCCAACGGCGGTGGTGTGACCAACCAACCATATAGGCGAAGACACCAGTCGGCGGCGACGGAGGCAGGCCG

Reverse complement sequence

CGGCCTGCCTCCGTCGCCGCCGACTGGTGTCTTCGCCTATATGGTTGGTTGGTCACACCACCGCCGTTGGGCGTCTACGACTTCACCGCCGGCCTGCCTC[T/C]
GTCGCCGCCGACTGGTGTCCCCGCCTACACGGTCGGTTGGTCACACCACCGTTGATGGGCATCGTCATCTACACCGCCGGCCTGCCTCCGTCGCCGCCGA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 70.60% 0.00% 10.64% 18.75% NA
All Indica  2759 54.80% 0.00% 16.20% 29.00% NA
All Japonica  1512 98.30% 0.10% 0.86% 0.73% NA
Aus  269 61.70% 0.00% 13.38% 24.91% NA
Indica I  595 24.40% 0.00% 14.12% 61.51% NA
Indica II  465 66.20% 0.00% 16.56% 17.20% NA
Indica III  913 70.10% 0.00% 17.74% 12.16% NA
Indica Intermediate  786 53.30% 0.00% 15.78% 30.92% NA
Temperate Japonica  767 98.70% 0.10% 0.78% 0.39% NA
Tropical Japonica  504 97.60% 0.00% 1.19% 1.19% NA
Japonica Intermediate  241 98.80% 0.00% 0.41% 0.83% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 83.30% 0.00% 7.78% 8.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0112723651 A -> G LOC_Os01g22620.1 missense_variant ; p.Cys260Arg; MODERATE nonsynonymous_codon ; C260R Average:19.746; most accessible tissue: Minghui63 panicle, score: 50.413 probably damaging -2.993 TOLERATED 0.44
vg0112723651 A -> DEL LOC_Os01g22620.1 N frameshift_variant Average:19.746; most accessible tissue: Minghui63 panicle, score: 50.413 N N N N