Approximately 30% of all distinct tags could be unambiguously mapped to a gene in the reference database and 60% of the distinct clean tags were mapped to the Gossypium genome database.
Initially, we just used the G. raimondii genome sequence for mapping tag sequences, about 23.6% of all distinct tags could be unambiguously mapped to a gene in the G. raimondii genome sequence, and about 45.2% of all distinct tags mapped to the genome (Additional file 7).
On the contrary, a well conserved divergent 3'-untranslated part sequence led to a common SAGE tag identified in zp2.3 and zp2.4 transcripts, while a distinct SAGE tag was recovered with zp2.2 (Tables 1 and 5).
In our study, more than 99% of the distinct tag entities showed the expression within a five-fold change between the two libraries (Additional file 5).
An average of 5.9 million sequence tags per library was obtained, with 507109 distinct tag sequences.
Low-expression tags with copy numbers smaller than 10 occupied the majority of distinct tag distributions (Additional file 7).
Approximately 5.7 to 6.1 million total sequence tags per library were obtained, with 20,000 to 70,000 distinct tag sequences.
The distribution of the various tag abundance categories between total and distinct tag counts was consistent across all libraries.
We also analyzed the distribution of the ratio of distinct tag copy numbers in each pair of libraries and found that more than 90% of the distinct tags had ratios up to 5-fold (Additional file 6: S6).
The distribution of the ratio of distinct tag copy numbers in each pair of libraries was analyzed.
