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Detailed information for vg0728251632:

Variant ID: vg0728251632 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 28251632
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 327. )

Flanking Sequence (100 bp) in Reference Genome:


CTGGTGGATTTGCCTTATCATGCAGGTACTCCAAACCCTTCGCTGCACCAACAGCAATCTTCATCCTTGCATTCCAGTCAAGAGGTTTCTTGCCTGGTGG[G/C]
CGATCTATTAAGAAAGTGCCCCATGAGTTATAAAATGATAGATAGCAATGTCTAAAGAAAATTAAATGTTGTCAGTAGCAAACTACAGTAAGACAGTGAA

Reverse complement sequence

TTCACTGTCTTACTGTAGTTTGCTACTGACAACATTTAATTTTCTTTAGACATTGCTATCTATCATTTTATAACTCATGGGGCACTTTCTTAATAGATCG[C/G]
CCACCAGGCAAGAAACCTCTTGACTGGAATGCAAGGATGAAGATTGCTGTTGGTGCAGCGAAGGGTTTGGAGTACCTGCATGATAAGGCAAATCCACCAG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(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 97.00% 3.00% 0.00% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 96.60% 3.40% 0.00% 0.00% NA
Indica III  913 93.50% 6.50% 0.00% 0.00% NA
Indica Intermediate  786 98.90% 1.10% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 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
vg0728251632 G -> C LOC_Os07g47270.1 synonymous_variant ; p.Arg167Arg; LOW synonymous_codon Average:45.137; most accessible tissue: Minghui63 flag leaf, score: 60.569 N N N N