Supplementary Report Metrics
The Supplementary Report contains data for the following metrics. Each metric appears on a per batch, per sample, or per region basis.
Metrics for Chromosome X only appear if you select the sex chromosome options Yes or SCA.
Value ranges appear as Minimum Value, Maximum Value surrounded by either parenthesis or brackets. Parenthesis indicate that an edge value is excluded from the range. Brackets indicate that an edge value is included in the range. Inf is an abbreviation for infinity.
|
Metric Name |
Frequency |
Description |
Type |
Regex or Value Range |
|---|---|---|---|---|
|
genome_assembly |
Per batch |
The system of coordinates for alignment of the sequencing data and report region coordinates. Always GRCh37 for VeriSeq NIPT Solution v2 – RUO. |
text |
^GRCh37$ |
|
frag_size_dist |
Per sample |
Standard deviation of the differences between actual and expected cumulative fragment size distributions. |
float |
(0, Inf) |
|
fetal_fraction |
Per sample |
Reported fetal fraction. |
float |
(0, 1) |
|
NCV_X |
Per sample |
Normalized chromosome value for X chromosome. Only appears if the sex chromosome reporting option allows for it. Otherwise, this metric appears as NOT TESTED. |
float |
(-Inf, Inf) |
|
NCV_Y |
Per sample |
Normalized chromosome value for Y chromosome. Only appears if the sex chromosome reporting option allows for it. Otherwise, this metric appears as NOT TESTED. |
float |
(-Inf, Inf) |
|
number_of_cnv_events |
Per sample |
Number of partial deletion or duplication regions detected in the sample. |
integer |
(0, Inf) |
|
non_excluded_sites |
Per sample |
Number of reads remaining after filtering, which are counted for analysis. |
integer |
(0, Inf) |
|
region_classification |
Per region |
Classification of the region by the system in the same format as the anomaly_description field in the NIPT Report. For chromosome X, if no reportable sex chromosome anomaly was detected, the region classification will match the value of class_sx in the NIPT Report. Value options (regex): DETECTED: (\+|-)[12]?[0–9] DETECTED: (del|dup)\([12]?[0–9]\)\(((p|q)[0–9]{1,2}(\.[0–9]{1,2})?){2}\) NO ANOMALY DETECTED DETECTED: (XO|XXX|XXY|XYY)|NO ANOMALY DETECTED - XX|NO ANOMALY DETECTED - XY|NOT REPORTABLE|CHR Y PRESENT|CHR Y NOT PRESENT |
text |
Values specified in Description. |
|
chromosome |
Per region |
The chromosome symbol. |
text |
chr[12]?[0-9X] |
|
start_base |
Per region |
First base included in the region. |
integer |
[1, Inf) |
|
end_base |
Per region |
Last base included in the region. |
integer |
[1, Inf) |
|
start_cytoband |
Per region |
Cytogenetic band of the first base included in the region. |
text |
(p|q)[0–9]{1,2}(\.[0–9]{1,2})? |
|
end_cytoband |
Per region |
Cytogenetic band of the last base included in the region. |
text |
(p|q)[0–9]{1,2}(\.[0–9]{1,2})? |
|
region_size_mb |
Per region |
The size of the region in megabases. |
float |
(0, Inf) |
|
region_llr_trisomy |
Per region |
The LLR (Log-Likelihood Ratio) score for trisomy for the region. Indicates the evidence for trisomy compared to the evidence for no change (disomy). A trisomy is called if this LLR score exceeds a predetermined threshold. For partial deletions or duplications, this metric only appears if the type is a gain (dup). Otherwise, this metric appears as not applicable (not applicable). |
float |
(-Inf, Inf) |
|
region_llr_monosomy |
Per region |
The LLR score for monosomy for the region. Indicates the evidence for monosomy compared to the evidence for no change (disomy). A monosomy is called if this LLR score exceeds For partial deletions or duplications, this metric only appears if the type is a loss (del). Otherwise, this metric appears as not applicable (not applicable). This metric appears as NOT TESTED if you choose to perform the basic screening type. |
float |
(-Inf, Inf) |
|
region_t_stat_long_reads |
Per region |
The t-statistic for the region. The t-statistic is the difference in coverage between the region and the rest of the genome, compared to the variation in the sample. This is a signal-to-noise metric that captures the detectability of any shift in coverage in the region. "long_reads" indicates that the coverage used for this t-statistic includes the full range of fragment sizes used in analysis. The t-statistic is combined with the fetal fraction estimated for the sample to generate LLR scores. |
float |
(-Inf, Inf) |
|
region_mosaic_ratio |
Per region |
The proportion of the fetal material that is aneuploid. This metric is based on the ratio of the fetal fraction inferred from the coverage of the region to the fetal fraction for the sample. In samples with fetal fractions close to zero, mosaic ratios can take negative values due to variability in the estimate of the sample fetal fraction used in their calculation. |
float |
(-Inf, Inf) |
|
region_mosaic_llr_trisomy |
Per region |
The LLR score for trisomy calculated using the fetal fraction inferred from the coverage in the region instead of the fetal fraction for the sample. For partial deletions or duplications, this metric only appears if the type is a gain (dup). Otherwise, this metric appears as not applicable (not applicable). |
float |
(-Inf, Inf) |
|
region_mosaic_llr_monosomy |
Per region |
The LLR score for monosomy calculated using the fetal fraction inferred from the coverage in the region instead of the fetal fraction for the sample. For partial deletions or duplications, this metric only appears if the type is a loss (del). Otherwise, this metric appears as not applicable (not applicable). This metric appears as NOT TESTED if you choose to perform the basic screening type. |
float |
(-Inf, Inf) |
