Extended Data Fig. 5: Full-length transcript coverage and differences in the distribution of nucleotides between SNPs and other positions enhance the evidence for the presence of a foreign transcript in the sampled tissue.

a, Sequenced transcripts would ideally have RNA-Seq reads covering most of the sequence, that is that all exons of the mRNA are approximately equally covered by sequenc- ing reads (top left). Reads covering all exons in the sample from Genotype 2 provide support for the whole transcript having moved from Genotype 1 to Genotype 2 across the graft junction. Transcripts with coverage only for a subsequence (bottom left) do not support full-length presence of the for- eign transcript. b, Neighbouring positions to SNPs can be used as a negative control to evaluate the strength of the signal at SNP positions. Shown here are neighbouring positions of the identified SNPs at the next nucleotide (SNP position +1). If the neighbouring position shows similar levels of alter- native nucleotides as the SNP position, the these are likely sequencing errors, rather than evidence for the alternate allele. If the SNP positions have a different frequency of Genotype 2 allele than the neighbouring position has errors, then there is evidence for the alternate allele. Analysing the fre- quencies of nucleotides at known SNP positions and their neighbours can aid data interpretation.