Table 1.

Summary of genes, splice junctions, and previously unrecognized TUs identified by RNA-Seq; mapping of the read for the merged lanes.

Mapping summaryHEK 293B cells
Total reads 8,638,919 7,682,230
Low-quality reads 234,160 194,999
Reads with multiple matches 1,546,361 1,324,770
Reads with unique matches 4,640,112 3,895,643
Reads mapping to annotated RNAs (ENSEMBL + Eldorado) 3,712,476 2,902,387
ENSEMBL genes with at least five reads 12,567 10,668
ENSEMBL genes with at least one read 14,963 13,739
Reads in intronic clusters 38,598 44,781
ENSEMBL genes with intronic read clusters 1445 1409
Introns with read clusters 1862 1847
Reads with no match to the genome 2,218,286 2,266,818
Reads aligned to splice junctions 307,904 229,453
    Identified junctions (expected) 78,880 (81,302) 62,596 (66,981)
    Genes (at least five reads) with junctions 10,292 8655
    Genes (at least one read) with junctions 10,558 8910
    Genes (at least one read) with previously unknown junctions 2078 1732
    Previously unknown junctions 2397 1965
    Previously unknown junctions identified by less than one read 203 182