Table 5.

Distribution of percentage of fusion reads across functional classes in cancer specific chimeric transcripts

chimer functional class	Min%	Max%	Average%	Median%
fusion-protein	0.00360	93.79	16.87	9.16
3′ truncated-protein	0.00034	99.64	15.19	6.54
cryptic splice-site	0.00600	99.83	17.50	4.37
novel RNA	0.00041	99.72	26.23	10.30

Percent of fusion reads was calculated as fusion (chimeric) transcript reads divided by total reads (fusion read count + wild-type (non-fusion) 5′-gene read count + wild-type (non-fusion) 3′-gene read count) (see Methods). RSEM estimated normalized read counts were used. Metric shown in the table were calculated using 1535 breast cancer specific chimer transcripts