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Detailed information for vg1227343228:

Variant ID: vg1227343228 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 27343228
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 313. )

Flanking Sequence (100 bp) in Reference Genome:


TTAGCAGACAGATGGAGATGGAACCAAACAAGTACTAGATCGTAGCAGCATACATACATCGCTCTGAGCTCGGTGCAGTTCTTGATCTCAGAAGGGATTG[G/A]
GCCATGCAAGCTGTTCTGGTGCAATGCTCTGAACAAAAGGGGTTAGAAATTAAAGAAAGACCAATGCGGATAGTGTAAATGAAGATGGTGTTGAAATGGG

Reverse complement sequence

CCCATTTCAACACCATCTTCATTTACACTATCCGCATTGGTCTTTCTTTAATTTCTAACCCCTTTTGTTCAGAGCATTGCACCAGAACAGCTTGCATGGC[C/T]
CAATCCCTTCTGAGATCAAGAACTGCACCGAGCTCAGAGCGATGTATGTATGCTGCTACGATCTAGTACTTGTTTGGTTCCATCTCCATCTGTCTGCTAA

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 97.90% 2.10% 0.00% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 93.50% 6.50% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 88.10% 11.90% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 96.70% 3.30% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 1.10% 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
vg1227343228 G -> A LOC_Os12g44090.1 missense_variant ; p.Pro131Ser; MODERATE nonsynonymous_codon ; P131S Average:61.844; most accessible tissue: Zhenshan97 panicle, score: 86.058 unknown unknown TOLERATED 0.95