The All Transcripts window has two tabs, each containing a table: Identified Transcripts and Novel Transcripts.
The table below describes each column type available in the All Transcripts window:
|
Column Name |
Description |
|
Assembly ID |
Name assigned to the assembled sequence, using the criteria specified in the wizard. |
|
Gene Name, Custom Column #1* |
Best matching gene meeting criteria defined in the wizard. |
|
Organism Name, Custom Column #2* |
Organism from which the best matching gene came. |
|
Accession Number, Custom Column #3* |
Accession number of the best match. |
|
Description, Custom Column #4* |
Description of the best match. |
|
Database |
Database (e.g. RefSeq, Custom, etc.) from which the best matching gene came. |
|
Transcript Length |
Length of the assembled sequence, in bases. |
|
Transcript Start |
Position in the assembled sequence where the match begins. |
|
Transcript End |
Position in the assembled sequence where the match ends. |
|
%Transcript Match |
Length of the matching segment in the transcript x 100, divided by the total length of the transcript. |
|
Gene Length |
Length of the database entry, in bases. |
|
% of Full Length |
Length of the assembled sequence x 100, divided by the length of the corresponding database entry. Values greater than 100% indicate that the assembled sequence is longer than the database entry. |
|
Gene Start |
Position in the database entry where the match begins. |
|
Gene End |
Position in the database entry where the match ends. |
|
% Gene Match |
Length of the matching segment in the database entry x 100, divided by the total length of the database entry. |
|
% Identity |
Total number of identical bases in the matching region x 100, divided by the total number of bases in the matching region. |
|
Bit Score |
Normalized value calculated from the raw score and expressed in units of “bits,” a common measure in information theory. |
|
eValue |
“Expectation value,” an estimate of the probability of obtaining the observed alignment score with two random sequences. Expectation values are less sensitive to length than Bit scores and are therefore are generally a better measure of alignment quality. |
|
Assembled Reads |
Total number of assembled reads for that sequence. |
*Custom columns: These four columns use default names (e.g., Gene name, Organism name) if one of the default RefSeq databases was used in the SeqMan NGen assembly. However, if you used a custom GREP expression or a custom database that did not include these fields, these columns may have different names or be absent from the table.