The Project Report for reference-guided assemblies will contain a subset of the following results:
| Run Statistics | |
|---|---|
| Reference Seq Cnt | The total number of sequences in the reference (template). |
| Sequence Cnt | The total number of reads in the sample. |
| Total Reads Assembled | |
| Pair Seqs Cnt | The number of paired sequences included in the assembly. |
| Single Pair Seq Cnt | The number of paired sequences of which only one pair was included in the assembly. |
| Split Seq Cnt | The number of sequences that were split in the assembly. |
| Bad Split Seq Cnt | The number of sequences that were split, and of which only one portion was included in the assembly. |
| Single Seq Cnt | The number of single (unpaired) sequences in the assembly. |
| Consistent Pair Cnt | The number of paired sequences that met pair constraints. One “pair” in this statistics represents two sequences. |
| Inconsistent Pair Cnt | The number of putative paired sequences that did not meet pair constraints. |
| Seqs score < 80% | Percentage of reads that exactly matched the template (i.e. “alignment score”). |
| Seqs score < 90% | |
| Seqs score < 100% | |
| Seqs score 100% | |
| Unassembled Sequences | |
| Unaligned Cnt | Total number of reads not included in the finished assembly. |
| LayoutMiss Cnt | The number of reads that didn’t match the template at all. In other words, the number of sequences that contained no mer which matched a mer on a template sequence. This number is affected by the assembly parameters merSize and merSkip. Example: A sequence that has no 21-mer in common with the template but does have a matching 17-mer would be included in LayoutMiss Cnt at a mer size of 21, but not at a mer size of 17. |
| LayoutPoor Cnt | The number of reads with an insufficient number of mer matches to be included in the assembly. This number is affected by the assembly parameter merLayoutMin. |
| Bad Seq Cnt | The number of reads with ≥25% ambiguous Ns in the sequence. Filtered Illumina data is sometimes included in this count, as well. |
| Excluded Seq Cnt | The number of contaminated reads. |
| ExcessiveCov. Seq Cnt | The number of reads unused due to excessive coverage. |
| SNP Info | |
| Found SNP Cnt (incl. indel lengths) | The number of SNP positions plus the total number of coalesced bases, minus the number of multi-base indel entries. |
| Found User SNP | The number of SNPs found that match those in the user-supplied VCF SNP file. |
| Missing User SNP coverage | The number of SNPs from the user-supplied VCF SNP file that were not found, even though the area had coverage. |
| Missing User SNP zero coverage | The number of SNPs from the user-supplied VCF SNP file that were not found because the area had no coverage. |
| Assembly Parameters | |
| merSize | The values specified in the SeqMan NGen wizard prior to assembly. |
| merSkip | |
| merSkipQuery | |
| merLayoutMin | |
| templateHitCntThresh | |
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