The Assembly Report for reference-guided assemblies will contain a subset of the following results:
|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%|
|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.|
|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.|
|merSize||The values specified in the SeqMan NGen wizard prior to assembly.|
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