Fig. 1: Copy number distribution of the Y chromosome palindromes in the Icelandic population.

A Y chromosome ampliconic regions. Top is a rectangular schematic of the entire Y chromosome. Below is a zoomed version of the mappable part of the male specific region of the Y chromosome, with the palindromes represented by labelled light blue triangles and the positions of genes shown below. Genes in red are known to be ampliconic and the grey shaded areas represent the centromere. Third is a further zoomed version of the ampliconic regions, again with the positions of palindromes and genes shown, and now also with amplicons shown as labelled coloured arrows. In the reference sequence of the human Y chromosome (NCBI build 38), the yellow amplicon (573,272 bp) has two copies (unique to palindrome P1), the green amplicon (307,076 bp) has three copies (two in P1 and one next to P2), the red amplicon (127,091 bp) has four copies (two in P1 and two in P2), the blue amplicon (167,703 bp) has four copies (two in P1 and two in P3), and the teal amplicon (115,689 bp) has two copies (unique to P3). B Copy number of the amplicons located in palindromes 1, 2 and 3. C Copy number of palindromes 4, 5, 6 and 8. D Mean minor allele read frequency (MARF) of paralogous sequence variants per male across the yellow amplicon shown in relation to copy number. E Number of paralogous sequence variants passing the filters used to calculate the MARF values presented in (D), shown in relation to copy number. F The structure of amplicons in the reference sequence and some of the known structural variants identified by previous studies, characterised deletions and amplification within the AZFc region. For deletions, the missing region is indicated with dotted lines. For duplications, the added region is indicated with a line delimiting the interval of the duplication.