Table 3.

Number of mapped sequencing reads for each different class of assembled transcripts

	LIM1	LIM2	LIM3	LIM4	LIM5	LIM6	LIM7	LIM8	LIM9
Code
e	841	898	884	711	904	757	655	547	741
=	26,052	26,029	26,072	26,075	26,237	26,064	2,6158	26,139	2,6117
x	285	276	250	227	278	271	195	177	247
s	2	2	4	2	5	3	3	2	3
j	9,262	9,660	9,476	9,008	7,811	9,121	8,111	8,223	8,753
c	2	2	2	2	2	3	3	2	3
p	714	629	678	693	749	711	529	670	615
u	1,459	1,510	1,988	1,123	1,842	1,462	868	1,058	985
.	3,577	3,411	3,585	3,274	3,690	3,674	2,344	2,079	3,296
o	413	434	448	377	354	427	317	288	362
i	1,611	1,701	2,271	1,316	2,369	1,725	967	603	1,446

e, single exon overlapping a reference exon and at least 10 bp of a reference intron indicating a possible pre-mRNA fragment; =, complete match of intron chain; x, exonic overlap with reference on the opposite strand; s, an intron of the transfrag overlaps a reference intron on the opposite strand (likely due to read mapping errors); j, potentially novel isoform; c, contained in reference; p, possible polymerase run-on fragment (within 2 kb of a reference transcript); u, unknown intergenic transcript; ., tracking file only, indicates multiple classifications; o, generic exonic overlap with a reference transcript; i, a single exon transcript falling entirely within a reference intron.