The Assembly Report for XNG 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 | |