Available Feature Table Columns

The table below describes each column type available in the Feature Tables. The first ten columns are available in all tables; the remaining options are available only in the Genes and/or CDSs and ncRNAs tables. To learn how to display, hide, rearrange or sort using these data columns, see Sorting and Rearranging Tables.

Workflow Available	Column	Description
All	Visible	A checkmark in this column indicates that the feature is currently displayed in the Alignment View (for features on constituent sequences) or the Strategy View (for features on the consensus sequence). The absence of a checkmark indicates that this feature is hidden. Note: The Visible column does not apply to variant features, which are available only in .sqd projects. To control the display of variants, select Variant > Show/Hide Variants. For more information, see Discovering Variants.
	Type	The feature type, or key, of the feature.
	Name	The name of the feature. The /dnas_title qualifier is used for the feature name. If no /dnas_title is available, SeqMan Pro will use the value of the first qualifier listed for the name.
	Location	The range of sequence associated with the feature, including gaps.
	Target Length	The target length of the fragment, equal to the end position minus the start position.
	Sequence	The name of the sequence that contains the feature.
	Coverage Depth	The average depth of coverage across the feature, calculated as the sum over all segments of the total number of bases covering each segment divided by the length of that segment. Note that the coverage for a gene may differ substantially from that of its corresponding CDS (e.g. exome or transcriptome sequencing). Values range from zero to the maximum coverage in the project and values are shown to the second decimal point to account for areas of very low, but non-zero coverage.
	Variant Count	The number of called variants in the feature. This number is determined using the default filtering parameters and is not updated by additional filtering in the Variants Summary Report. Note that, for example, a gene feature in an exome project can have a very low Coverage Depth value and still have one or many variants.
Genes only	Total raw count	The total number of reads which were initially, uniquely assigned to any isoform within the gene.
Genes only	Total_repeat_distrib_count	The total count of reads which were proportionally distributed to any isoform within the gene.
Isoforms only	Raw_count	The number of reads that were initially and uniquely assigned to an isoform, fragment or peak. This value is not normalized and does not account for repeat reads.
	Count	The total number of aligned reads assigned to an isoform feature, after adjustments for repeat distribution.
	Raw_repeat_count	The total fraction of repeat reads that map to the peak. For example, if one read maps equally well to two peaks, each peak would have a Raw_repeat_count of 0.5. If multiple repeat reads map to a single peak, the proportions are summed to get the Raw_repeat_count. This column is only available if repeat handling was specified in SeqMan NGen.
	Repeat_distrib_count	The proportional number of repeated reads assigned to this exon, gene or isoform.
	Repeat_distrib_percent	A rough estimate of the percentage of the total repeated reads which could have been assigned and that were assigned. In other words, the percentage of Repeat_distrib_count in Raw_repeat_count.
RNA-Seq projects only. For isoforms, the word “total” is omitted from the column name.
Stranded only	Coverage Strand Depth	The total number of sequenced bases within the feature and on the correct strand, divided by the length of the feature.
RPKM normalization specified	Total RPKM	Reads assigned per kilobase of target per million mapped reads (RPKM) = The signal values for each experiment divided by the total bases of target sequence divided by one thousand; the resulting number is then divided by the total number of mapped reads divided by one million.
RPKM normalization specified	Replicate set total RPKM	The RPKM value averaged over the set of replicate samples. Only available if replicates and replicate sets were specified in SeqMan NGen.
RPM normalization specified	Total RPM	Reads assigned per million mapped reads (RPM) = The signal values for each experiment divided by the total number of mapped reads divided by one million.
RPM normalization specified	Replicate set total RPM	The RPM value averaged over the set of replicate samples. Only available if replicates and replicate sets were specified in SeqMan NGen.
RPK normalization specified	Total RPK	RPK (reads assigned per kilobase of target) = The signal values for each experiment divided by the total bases of target sequence divided by one thousand.
RPK normalization specified	Replicate set total RPK	The RPK value averaged over the set of replicate samples. Only available if replicates and replicate sets were specified in SeqMan NGen.
No normalization specified	Total_count	The sum of the counts for all of the isoform features within a gene.
No normalization specified	Replicate set total count	The total number of aligned reads averaged over the set of replicate samples. Only available if replicates and replicate sets were specified in SeqMan NGen.