Modifying the Gene CNV report

NextGENe Online Help : NextGENe Viewer Comparison Reports and Tools : The CNV (Copy Number Variation) Tool : To generate the CNV Tool report : Gene CNV report : Modifying the Gene CNV report

Do one or both of the following:

• For the Filter settings, specify the thresholds for the regions that are to be included in the report.

• For the Display settings, select the columns that are to be included in the report, or clear the options for the columns that are not to be included.

Setting	Description
Display settings
Index	An ordered count of the segments that are used in the report.
Chr • Name • Number	• The name of the chromosome that the segment is on. • The number of the chromosome that the segment is on.
Chr Position Start	The base number that indicates where the segment starts in the chromosome.
Chr Position End	The ending base number that indicates where the segment ends in the chromosome.
Gene	The gene name for the segment when the segment is the whole gene or the name of the gene on which the segment is found.
CDS	The coding sequence number for the segment.
RNA Accession	Show the RNA accession for the gene from NCBI.
Protein Accession	Show the protein accession for the gene from NCBI.
Description	Available if the reference file is a .fasta file with multiple segments. Select this option to display the title line for each segment in the Description column.
Contig	The contig on which the segment is located. The contig is based on the genome assembly from the NCBI.
Locus Tag	An alternate way to identify the gene.
Start	The starting location for the reference region.
End	The ending location for the reference region.
Length	The total length of the reference region, which provides for easy identification of expressed regions by size (such as when locating small RNA transcripts).
Original Coverage	The actual median coverage for the region in each sample.
Normalized Coverage	The median coverage following global normalization for the region in each sample.
Position Selected	The median coverage position for the region. This position is used for the calculation of the Log2 Ratio.
Control Allele	Read count for the alleles at the Position Selected in the control project. If there are more than two alleles, then only the two most frequent alleles are reported.
Sample Allele	Read count for the alleles at the Position Selected in the sample project. If there are more than two alleles, then only the two most frequent alleles are reported.
Log2 Ratio	The Log2 of the ratio of the normalized coverages of the two sample files.
Neighbor Ratios	The Log2 ratios for the current region followed by the Log2 ratios of the neighbor regions.
Filter settings
Log2 Ratio <= [-0.700] or >= [0.700}	Display only those regions where the Log2 of the ratio of the normalized coverages of the two sample files is above or below the set thresholds. The Log2 ratio for each of the consecutive regions must fall above or below the indicated thresholds.
Scores >= [3.000]	Show only regions where the Phred-scaled score for at least one potential call (insertion, deletion, or normal) meets or exceeds the set threshold. The score for each of the consecutive regions must exceed the indicated threshold.
Show Regions with Low Coverage	Select this option to include the regions that do not meet the minimum coverage threshold in the report.
Minimum Coverage >= [5]	Include regions that meet or exceed the indicated coverage level in the report.
Show Gene Exon Number >= [1]	The minimum number of consecutive regions where the Log2 ratios exceed the defined thresholds for the regions to be included in the report.