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Table 2 Summary of polymorphism analysis

From: SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines

Parameter Value Comments
Number of loci screened 18  
Total length of amplicons, bp. 6935 2349 coding, 4586 non-coding
Number of bases of sequence screened, bp. 213999  
Number of all sequence variants (SNPs and Indels) 169 1 per 41 bp
Number of nucleotide substitutions 114  
Transitions / Transversions ratio 1.53  
Frequency of polymorphic sites per bp 0.0164 1 per 60.8 bp
Frequency of polymorphic sites per bp (coding) 0.0077 1 per 130.5 bp
Frequency of polymorphic sites per bp (non-coding) 0.021 1 per 47.7 bp
Number of Indels 55  
Overall indel frequency 0.0079 1 per 126.1 bp
Frequency of indels per bp (coding) 0.0004 1 per 2349 bp
Frequency of indels per bp (non-coding) 0.0118 1 per 85 bp
Mean nucleotide diversity (π) 0.0063  
Mean nucleotide expected heterozygosity 0.26  
Mean haplotype expected heterozygosity 0.56  
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