Analysis Reports
The BWA Whole Genome Sequencing app provides an overview of statistics per sample on the sample pages. A brief description of the metrics is below.
Alignment Summary
| Statistic | Definition |
|---|---|
| Number of reads | Total number of reads passing filter for this sample. |
|
Coverage |
Total number of aligned bases divided by the genome size. |
|
Percent Duplicate Paired Reads |
Percentage of paired reads that have duplicates. |
|
Fragment Length Median |
Median length of the sequenced fragment. The fragment length is calculated based on the locations at which a read pair aligns to the reference. The read mapping information is parsed from the BAM files. |
|
Fragment Length Standard Deviation |
Standard deviation of the sequenced fragment length. |
| • | Read Statistics |
| Statistic | Definition |
|---|---|
|
Percent Aligned |
Percentage of reads passing filter that aligned. |
| Percent Q30 | The percentage of bases with a quality score of 30 or higher. |
|
Mismatch Rate |
The average percentage of mismatches across both reads 1 and 2 over all cycles. |
Small Variants Summary
This table provides metrics about the number of SNVs, insertions, and deletions.
| Statistic | Definition |
|---|---|
|
Total Passing |
Total number of variants present in the data set that pass the variant quality filters. |
|
Percent found in dbSNP |
100*(Number of variants in dbSNP/Number of variants). |
|
Het/Hom Ratio |
Number of heterozygous variants/Number of homozygous variants. |
|
Ts/Tv Ratio |
Transition rate of SNVs that pass the quality filters divided by transversion rate of SNVs that pass the quality filters. Transitions are interchanges of purines (A, G) or of pyrimidines (C, T). Transversions are interchanges between purine and pyrimidine bases (for example, A to T). |
Variants by Sequence Context
| Statistic | Definition |
|---|---|
| Number in Genes | The number of variants that fall into a gene. |
| Number in Exons | The number of variants that fall into an exon. |
| Number in Coding Regions | The number of variants that fall into a coding region. |
| Number in UTR Regions | The number of variants that fall into an untranslated region (UTR). |
| Number in Splice Site Regions | The number of variants that fall into a splice site region. |
| Number in Mature microRNA | The number of variants that fall into a mature microRNA. |
Variants by Consequence
| Statistic | Definition |
|---|---|
| Frameshifts |
The number of variants that cause a frameshift. |
| Non-synonymous | The number of variants that cause an amino acid change in a coding region. |
| Synonymous | The number of variants that are within a coding region, but do not cause an amino acid change. |
| Stop Gained | The number of variants that cause an additional stop codon. |
| Stop Lost | The number of variants that cause the loss of a stop codon. |
Structural Variants Summary
This table breaks structural variant output into the classes of variants called, and reports the total number and their overlap with annotated genes. All counts are based on PASS filter variants.
| Variant Class | Definition |
|---|---|
| CNV |
Number of copy number variations.
|
| Insertions | Number of insertions |
| Tandem duplications | Number of tandem duplications |
| Deletions | Number of deletions |
| Inversion | Number of inversions |
Coverage Histogram
The coverage histogram shows the number of reference bases plotted against the depth of coverage (read depth). It has the following features:
| • | The dropdown menu allows you to look at the overall picture, or highlight a particular chromosome. |
| • | The Fix Y Scale checkbox allows you to keep the Y Scale the same when comparing multiple chromosomes. |
| • | The Export TSV link allows you to export the coverage data in a tab-separated TXT file. |
Figure 4 BWA Whole Genome Sequencing Coverage Histogram
