Additional file 3: of A frameshift mutation in ARMC3 is associated with a tail stump sperm defect in Swedish Red (Bos taurus) cattle

Structural sequence variants that were compatible with recessive inheritance. Grey background indicates an intergenic sequence variant that was not polymorphic among 1147 animals of the 1000 bull genomes project. (XLSX 36 kb

Additional file 4: of A frameshift mutation in ARMC3 is associated with a tail stump sperm defect in Swedish Red (Bos taurus) cattle

Genotype distribution of 73 candidate causal mutations for the tail stump sperm defect in 1147 animals from the 1000 bull genomes project. Alternate allele frequency and genotype distribution of 73 variants in 29 breeds (homozygous animals for the reference allele | heterozygous animals | homozygous animals for the alternate allele). Grey color indicates variants that were considered as candidate causal mutations. Red color indicates the deletion mutation in the coding sequence of ARMC3. (XLSX 49 kb

Association of 2101 autosomal CNVs with the affection status of 94 animals.

<p>The presence of CNV segments was compared in 21 cases and 73 controls using Fisher exact tests. The dots represent SNPs within the CNV segments. Red dots represent SNPs in significantly overrepresented CNVs in cases vs. controls (P < 2.38 x 10^-5).</p

Additional file 2: of A frameshift mutation in ARMC3 is associated with a tail stump sperm defect in Swedish Red (Bos taurus) cattle

Sequence variants identified using the SAMtools software package that were compatible with recessive inheritance. Grey background indicates 15 sequence variants that were not polymorphic among 1147 animals of the 1000 bull genomes project. Red color indicates a coding variant compatible with recessive inheritance. The functional consequence of the alternative allele was predicted using the Variant Effect Predictor from Ensembl (see Methods). (XLSX 61 kb

Schematic view of two CNV segments on BTA6 and BTA29.

<p>The figures display 5-SNP-sliding-window log R ratios in 75 unaffected (grey) and 21 affected (blue) animals on BTA6 (A) and BTA29 (B). The grey shaded box represents the extent of the two CNV segments. The gene content was assessed based on the University of Maryland assembly.</p

Association of 647,971 SNPs in four different case control scenarios.

<p>The Manhattan plots represent the -log₁₀(P) values of association for 647,971 SNPs in four different case-control designs (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075659#pone-0075659-t001" target="_blank">Table 1</a>). The red dots represent significantly associated SNPs (P < 7.71 x 10^-8).</p

Left-sided gonadal hypoplasia.

<p>(A) Hypoplastic ovary (left arrow) and normal ovary (right arrow). (B) Hypoplastic testicle (left) and normal testicle (right).</p