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On chromosome 6, the short arm had more polymorphic InDels than the long arm.
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Lai et al. re-sequenced a group of six elite maize inbred lines, and uncovered more than 30,000 polymorphic indels with sizes smaller than six bp [ 19].
Three clones were sequenced for each individual when sequences contained two or more polymorphic sites and/or an unpaired indel (an indel of a different length).
There were 162,380 highly polymorphic InDels with a polymorphism information content (PIC) ≥ 0.5, contributing 1.81 % to the unique primer set.
Finally, we experimentally validated 100 highly polymorphic InDels for accuracy and polymorphism.
Aligned sequences for all isolates, excluding the indels, demonstrated that the IGS region was more polymorphic and had greater nucleotide diversity between the 2 genomic groups than did the other loci (Table 2).
A total of 24 polymorphic indels and 1205 single-nucleotide polymorphisms (SNPs) were detected.
However, the IGS sequences were more polymorphic between the 2 genomic groups than were the other loci, and the indels in this region created unique sequences in GGII isolates that were absent in GGI isolates.
First, whole-genome sequences of more than a thousand human individuals from the 1000 Genomes Project (TGP) [ 12] were used to identify polymorphic INDELs.
Of these highly polymorphic InDels, we also selected InDels with major allele differences (the size difference between the most and second most frequent alleles) ≥ 3 bp or 8 bp for primer design, which provided a more flexible choice for researchers.
For different resolutions of polyacrylamide gel electrophoresis and agarose gel electrophoresis, two sets of highly polymorphic InDel markers were selected from 162,380 highly polymorphic InDels with PIC ≥ 0.5.
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