Table S2.

Summary of high-throughput RNA sequencing analysis

Library	Total reads	Total matches (% of total)*	Reads mapped to splice junctions (% of total)	Unique matches (% of total matches)†	Multiple matches (% of total matches)‡	Coverage of intron-containing genes (RPKM > 3)§	Coverage of genes (RPKM > 3)§
Col	29,505,966	27,908,233 (94.6%)	8,769,813 (29.5%)	27,440,647 (98.3%)	467,586 (1.7%)	13,308	15,300
atprmt5-2	31,472,542	29,483,401 (93.7%)	9,334,131 (29.5%)	28,919,312 (98.1%)	564,089 (1.9%)	13,345	15,225
atprmt5-2 prp8-8	30,418,678	28,703,813 (94.3%)	8,948,627 (29.3%)	28,170,586 (98.1%)	533,227 (1.9%)	13,178	15,077
atprmt5-1 prp8-9	30,146,556	28,116,182 (93.3%)	8,427,608 (27.9%)	27,669,011 (98.4%)	447,171 (1.6%)	12,254	13,915

RPKM, reads per kilobase per million mapped reads.

^*Number of reads that aligned to the A. thaliana genome and annotated splicing junction sequences.

^†Number of reads that aligned to a unique location of the TAIR9 reference genome.

^‡Number of mapped reads that aligned to more than one genomic location.

^§Number of intron-containing genes covered by the unique reads (>3 RPKM).