Table 2. Summary Statistics of RNA-Seq Alignment.

	# Reads Total (millions)	# Mapped Reads (millions)	Mapped Reads (% of Total)	# Annotated Mapped Reads (millions)	Annotated Mapped Reads (% of Total)	# Annotated Uniquely Mapped Reads (millions)	# Annotated Exactly Mapped Reads (millions)
155-1 (NE-45)	173	167	96.5	113	65.3	37.7	20.5
155-2 (RB-07)	79.6	76.4	96.0	65	81.7	23.8	9.9
155-3 (FS-25)	54.8	52.2	95.3	47.2	86.1	22.4	13.1
155-4 (FS-22)	76.6	73.6	96.1	63.6	83.0	25.1	9.9
155-6 (3024l)	61.6	58.0	94.2	51.4	83.4	20.8	9.7
155-7 (0063)	73.6	69.0	93.8	61.8	84.0	26.2	13.5
157-1 (RB-10)	106	99.4	93.7	81.2	76.6	32.5	13.1
157-2 (NE-42)	114	108	95.0	91.2	80.0	34.0	12.3
157-3 (NE-41)	99.8	94.2	94.4	78.6	78.8	39.4	16.4
157-4 (RB-03)	108	102	94.4	92.2	85.4	42.5	20.6
157-5 (FS-21)	112	105	93.6	95.8	85.5	30.4	12.5
157-6 (RB-16)	148	141	95.2	126.2	85.3	57.2	29.3
157-7 (3024r)	134	126	93.7	102.8	76.7	34.6	14.2
157-8 (2970)	94.0	87.6	93.2	78.8	83.8	31.8	16.0

Code 155 designates flow cell A, code 157 designated flow cell C, followed by the lane number. The sample ID is in parentheses. Normal samples are bolded. Annotated mappings result from Bowtie alignment with the Ensembl 63 GTF file. Uniquely mapped reads are mapped to only one region of the genome by the Bowtie aligner, and exactly mapped reads map to only one location and have no mismatches to the reference.