This is an example analysis using the 26 000 ESTs published by Torres et al. 2008. The ESTs were mapped to the D. melanogaster genome and SNPs were identified without using quality sequences.
| general information | Displays general information about the analysis. Important: This also contains the SNP-benchmarks |
| strand | either the original or the reverse complement of an EST may align with a reference gene. Choose whether you want to include SNPs being derived from EST which are aligned unchanged or as reverse complement |
| min. tags gene | minimum number of ESTs mapping to the reference sequence (gene) |
| min. tags SNP-site | minimum number of ESTs mapping to a SNP-site. SNP-sites with less tags are not considered. |
| min. alleles | minimum number of alleles at a SNP-site |
| max. alleles | maximum number of alleles at a SNP-site |
| min. PIC | minimum PIC at a SNP-site |
| min. dist | minimum distance from the alignment end for each individual SNP |
| max. low qual. | maximum number of low alignment quality tokens in the neighborhood of a SNP ('-','N'). When the 454-adapted mode was used, this feature can be used to restrict the number of homopolymers in the immediate neighborhood of a SNP. For example when this value is set to 2 only one homopolymer of length 3 or two homopolymers of length 2 are allowed in the neighborhood. see details |
| min. qual. site | minimum sequence quality at SNP |
| min. qual. neigh | minimum average sequence quality in the neighborhood of a SNP |
| clipboard | copy the analysis to the clipboard |
| export subset | export the active subset of SNPs or SNP-sites |
| update analysis | update the analysis using the user-specified parameters |
| results | the results of the analysis |
The following example is derived using the data published by Torres et al. 2008 .
| FBgn0013686 | 2665 | 1429 | 10 | 2068 | 999 | 10 | 83.51 |
| FBgn0013674 | 340 | 226 | 3 | 77 | 77 | 3 | 96.58 |
| FBgn0013676 | 71 | 71 | 1 | 67 | 67 | 1 | 98.51 |
| FBgn0013678 | 64 | 22 | 6 | 56 | 20 | 6 | 66.07 |
| a | b | c | d | e | f | g | h |
| a | the ID of the reference sequence (gene ID) ; database sequence ID |
| b | number of SNPs at the reference sequence |
| c | number of all ESTs (tags) having a SNP. Not every EST mapping to a gene will also map to a SNP-site |
| d | number of SNP-sites at the reference sequence |
| e | active subset: number of SNPs at the reference sequence |
| f | active subset: number of ESTs having a SNP |
| g | active subset: number of SNP-sites at the reference sequence |
| h | percent of SNPs being derived from ESTs which are aligned to the reference sequence without reverse complementig the EST. In short: percent of sense SNPs; for active subset |
Torres TT, Metta M, Ottenwälder B, Schlötterer C.
Gene expression profiling by massively parallel sequencing.
Genome Res. 2008 Jan;18(1):172-7. Epub 2007 Nov 21.