Table 2. Alignment of Illumina-Solexa 50 bp single end reads onto the Corydalis reference transcriptome.

Bulb stage	Day 0	Day 10	Day 30
Total raw reads	7142394	7595670	7043080
Total clean raw reads	7045623 (98.65%)	7504270 (98.80%)	6933847 (98.45%)
Total mapped clean reads	4206094 (59.70%)	4161699 (55.46%)	3112053 (44.88%)
Perfect match	3270224 (46.41%)	3224934 (42.97%)	2383576 (34.38%)
≤2 bp mismatch	935870 (12.28%)	936765 (12.48%)	728477 (10.51%)
Unique match	4199436 (59.60%)	4155601 (55.38%)	3106357 (44.80%)
Multi-position match	6658 (0.09%)	6098 (0.08%)	5696 (0.08%)
Mapped reference genes	45289 (96.19%)	45547 (96.74%)	44831 (95.22%)
Unigenes with RPKM ≥ 2.00	42454(93.74%)	42913(94.22%)	42162(94.05%)