Partial AZFc deletion sub-types in samples belonging to haplogroup R (reference sequence). The blue (b), green (g), red (r) and yellow (y) families contain multiple copies of the PRY, BPY2, DAZ and CDY1 genes, respectively, with purportedly different functional capabilities between copies. Black box: present region; white box: absent region; grey box: multiple-copy marker that is considered absent in that specific position according to the deletion context; diagonal lines box: multiple-copy marker for which data is not sufficient to confirm either presence or absence; crossed box: marker present due to previous inversion event occurring between the b2 and b3 amplicons. Letters A-C denote the AZFc background where the deletions occurred. A- Reference AZFc sequence. B- b2-b3 inversion in the reference AZFc sequence, as previously described. C- y1-y2 inversion in the reference AZFc sequence. This AZFc background is proposed as the most parsimonious for the observed deletion products, yet no fluorescence in situ hybridization confirmation of this rearrangement is possible due to the symmetry of the inversion. Average sperm count of oligozoospermic men is indicated in parentheses (in million sperm/ml). a- Sample with additional sequence conversions in the b2 and g2 markers. b- The deletion breakpoint (mapped between exons 4 and 10 of DAZ1/DAZ3) is more distal than in the 3 previous samples. c- Sample with sequence conversion leading to the loss of the b2-specific variant. d- Sample with sequence conversion leading to the loss of the g3-specific variant. e- Sample with sequence conversion leading to the loss of the b4-specific variant. [For complete marker profiles and full haplogroup nomenclature please see Additional file 1].