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Detailed information for vg1200521290:

Variant ID: vg1200521290 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 521290
Reference Allele: AAlternative Allele: C
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTTCACATGTTGCCTATTTTGATCTTGGAACGAAATTTCATTGACCCATGTCTAACACGACATAATCCTTCTCTTCGATTCTCATCGGTAGCGGCGGCGC[A/C]
TCAACGGCGACGATGCAGCCTTCTCTCTCCAAAGGCGCCATCGCCGCCTCCTCCTCCTCCTCCTCGCCACCTTTGGCGTACAGCACGTCCTCCTCCACGT

Reverse complement sequence

ACGTGGAGGAGGACGTGCTGTACGCCAAAGGTGGCGAGGAGGAGGAGGAGGAGGCGGCGATGGCGCCTTTGGAGAGAGAAGGCTGCATCGTCGCCGTTGA[T/G]
GCGCCGCCGCTACCGATGAGAATCGAAGAGAAGGATTATGTCGTGTTAGACATGGGTCAATGAAATTTCGTTCCAAGATCAAAATAGGCAACATGTGAAA

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 95.00% 4.20% 0.72% 0.00% NA
All Indica  2759 96.90% 1.90% 1.20% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 47.20% 52.40% 0.37% 0.00% NA
Indica I  595 95.30% 0.00% 4.71% 0.00% NA
Indica II  465 99.40% 0.40% 0.22% 0.00% NA
Indica III  913 98.80% 1.20% 0.00% 0.00% NA
Indica Intermediate  786 94.50% 5.00% 0.51% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 95.60% 4.40% 0.00% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1200521290 A -> C LOC_Os12g01890.1 missense_variant ; p.Asp398Glu; MODERATE nonsynonymous_codon ; D398E Average:65.315; most accessible tissue: Zhenshan97 flower, score: 84.018 benign 0.871 TOLERATED 0.82