SamTools

Mapped reads per contig

Figure 1 : graph of the proportion of each sample allocated to different chromosomes in normalised counts.

source : nf-core RNAseq MultiQC

In Figure 1, chromosomes are indicated on the x-axis and the normalized quantity on the y-axis.

Samtools idxstats provides information on the alignment of sample reads/contigs after their alignment to different parts of the reference genome.

For the human genome, the numbered chromosomes become progressively smaller, so it is normal to see a decreasing trend along the x-axis. The Y chromosome is noted as 0 here, but it is identified, simply at a ratio so low compared to the others (ratio < 0.01%) that it is not represented.

For RNAseq data, the “MT” part corresponds to the mitochondrial genome and can show very high ratios due to the significant expression of these organites.