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Detailed information for vg1202831209:

Variant ID: vg1202831209 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 2831209
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 340. )

Flanking Sequence (100 bp) in Reference Genome:


TTTCCAAACGAAGTTACCTATCTCTCCATCTTGTCAGCATGCAGTCATACTGGCTTAGTTGAAGAGGGCCGTCACTACTTTAACCTGCTATTGTCTGATC[G/A]
GACCGCTGAACCTAATGTCCTTCACTATTCTTGTATGGTTGATGTTTTGGGGCGATCTGGGAAGACTGATGAGGCTTGGAAATTACTTGATAAAATGCCA

Reverse complement sequence

TGGCATTTTATCAAGTAATTTCCAAGCCTCATCAGTCTTCCCAGATCGCCCCAAAACATCAACCATACAAGAATAGTGAAGGACATTAGGTTCAGCGGTC[C/T]
GATCAGACAATAGCAGGTTAAAGTAGTGACGGCCCTCTTCAACTAAGCCAGTATGACTGCATGCTGACAAGATGGAGAGATAGGTAACTTCGTTTGGAAA

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 98.20% 1.80% 0.00% 0.00% NA
All Indica  2759 99.30% 0.70% 0.00% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 76.20% 23.80% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 99.40% 0.60% 0.00% 0.00% NA
Indica III  913 99.80% 0.20% 0.00% 0.00% NA
Indica Intermediate  786 98.20% 1.80% 0.00% 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  96 100.00% 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
vg1202831209 G -> A LOC_Os12g06070.1 missense_variant ; p.Arg389Gln; MODERATE nonsynonymous_codon ; R389Q Average:49.23; most accessible tissue: Callus, score: 83.761 benign 0.067 TOLERATED 0.19