TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

Table 5 Expression levels of genes with pseudogene copies from Chen et al. [11].^a

Number of pseudogene copies^b	Gene with pseudogene copies (%)^c	Pair count, %^d	Ratio^e	Normalized count, %^f	Normalized ratio^f
1	553 (1.7%)	6.85	× 4.02	9.37	× 5.49
2	113 (0.4)	5.15	× 14.79	5.20	× 14.93
3	49 (0.2)	1.27	× 8.38	1.96	× 12.99
4	27 (0.1)	2.27	× 27.32	2.28	× 27.35
≥ 5	130 (0.4)	6.91	× 17.24	8.08	× 20.16
Total (≥ 1)	872/32,439 (2.7)	22.45	× 8.35	26.88	× 10.00

^aUsing Bowtie2, we aligned RNA-seq paired-end reads to 32,439 annotated genes.
^bNumber of pseudogene copies of a gene. The first row shows genes that have just one pseudogene, followed by rows for genes with two, three, four, and at least five pseudogene copies.
^cNumber of genes with the specified number of pseudogene copies; for example, 553 genes (1.7% of all genes) have one pseudogene copy.
^dPercentage of read pairs that were mapped to genes with pseudogene copies.
^eRatio of columns 3 and 2.
^fThese two columns were similarly defined using a normalized count, where the number of reads mapping to each gene was normalized to account for gene length.

ISSN: 1474-760X