The gene-based partition tends to result in low sig-mer coverage for genes sharing similar sequences.
The minimum k-mer coverage for each unigene was 400 (Fig. 2B), and 88% of contigs were covered for >1,000 k-mer of 63 bases.
For a male fetus, we first supposed that chromosome Y is monosomic and extrapolated the fitted k-mer coverage for chromosome X, with the fetal DNA fraction estimated only by the k-mer coverage of chromosome Y.
Because of the differences among the samples, we normalized the data and computed the relative k-mer coverage for each sample as r i, j = C i, j C i, where C – i = 1 22 ∑ j = 1 22 C i, j was the average k-mer coverage of the 22 autosomes in the i-th sample.
We computed the k-mer coverage for each chromosome and every sample, as C i, j = n i, j N i where is the ID of control samples; j is the chromosome ID; ni,j is the number of unique reads mapped onto chromosome j from sample i and Ni,j was the total number of unique reads for chromosome j.
We calculated the fitted relative k-mer values for the sex chromosome analysis as follows: cr′ i, j, m = f j, m (GC i, j ) · (j = X, Y), for the fitted relative k-mer coverage from a regression of an adult male data set; and cr′ i, j, f = f j, f (GC i, j ) · (j = X, Y), for the fitted relative k-mer coverage from a regression of a fetal-female data set.
For L. fleischmannii, the median K-mer coverage of all contigs was 42.5, whereas ssu and lsu rDNA contigs had coverage of 263 and 290, respectively, again indicating the presence of 6 or 7 copies of the ribosomal repeat.
Scalpel applied the standard formula for the Chi-Square statistics and applied to the K-mer coverage of both alleles of an INDEL.
Default parameters were implemented except for maximum coverage of 50 in the normalization step and a minimum k-mer coverage of 20 as well as a minimum contig length of 300 in the assembly step.
For L. newyorkensis, contigs representing small and large subunit ribosomal DNA sequences had K-mer coverage of 328 and 385, respectively, with the median K-mer coverage of all contigs being 55, consistent with the presence of 6 or 7 copies of the ribosomal repeat.
A k-mer count (k = 25) of mtDNA reads showed a peak at a multiplicity at 52,000 (the mean k-mer coverage of the sequencing data), representing a mean depth of sequencing coverage of 68,000X (see Materials and Methods for details of this calculation).
