Calculating general statistics and determining genetic sex

Samtools 1.3 (68) option stats was used to determine the number of final reads, average read length, average coverage, etc. Genetic sex was calculated using the script sexing.py from (75), estimating the fraction of reads mapping to chrY out of all reads mapping to either X or Y chromosome.

The average coverage of the whole genome for the samples is between 0.00004× and 5.03× (table S1). Of these, 2 samples have an average coverage of >0.01×, 18 samples have >0.1×, 9 samples have >1×, 1 sample have around 5×, and the rest are lower than 0.01× (table S1). Genetic sexing confirms morphological sex estimates or provides additional information about the sex of the individuals involved in the study. Genetic sex was estimated for samples with an average genomic coverage of >0.005×. The study involves 16 females and 20 males (Table 1 and table S1).