Table 5

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

Number of pseudogene copiesb

Gene with pseudogene copies (%)c

Pair

count, %d

Ratioe

Normalized count, %f

Normalized ratiof


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.

Kim et al. Genome Biology 2013 14:R36   doi:10.1186/gb-2013-14-4-r36

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