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Tpi and Ci show many polymorphic indels, and strong evidence for recombination between haplotypes.
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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.
A total of 24 polymorphic indels and 1205 single-nucleotide polymorphisms (SNPs) were detected.
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.
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.
Alignment artifacts may be responsible for complex patterns of fixed segregating sites and indels overlapping SNPs and polymorphic indels.
In other words, SNPs are strongly positively correlated with polymorphic indels but not so much to fixed human indels or chimp indels (and so on).
We trained a model using all windows without polymorphic indels (42214 windows).
This interpretation is not corroborated by our results as only polymorphic indels are strongly underrepresented on the X-chromosome.
In this vein, we obtain where Sfix, Ifix, Spoly, and Ipoly represent the numbers of fixed substitutions, fixed indels, polymorphic substitutions, and polymorphic indels, respectively.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com