The Project Report for reference-guided assemblies will contain a subset of the following results:
Run Statistics | |
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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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