# Target Files Error Code

***

#### Genotyping <a href="#genotyping" id="genotyping"></a>

| Error Code | Description                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     |
| ---------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| 101        | Flanking sequence is too short.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 |
| 102        | <p>Polymorphism or sequence formatting error.<br><br>Possible causes can include:</p><ul><li>Incorrect polymorphism format. Example: SNP => \[X/Y], INDEL => \[-/XYZ], CpG => \[CG].</li><li>More than one set of brackets in a sequence.</li><li>Missing brackets around polymorphism format.</li><li>SNP alleles are not separated by a /.</li><li>Spaces in a sequence.</li></ul><p><br>Possible solution:</p><ul><li>Correct the issue and resubmit your target file.</li></ul>                                                                                                                                                                                                                                                                                                                                                                                                             |
| 103        | <ul><li>Cannot determine the top/bot strand.</li><li>Low sequence complexity.</li></ul>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         |
| 104        | <p>Polymorphism is not appropriate for the Illumina platform.<br><br>Possible causes can include:</p><ul><li>Tri- or quad-alleic SNP.</li><li>Contains characters other than A, G, C, T.</li></ul>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              |
| 105        | <p>Polymorphism is on the mitochondrial genome. Illumina does not recommend using mitochondrial polymorphisms for oligo pools.<br><br>Possible solution:</p><ul><li>Remove any polymorphism on the mitochondrial DNA from your target file and resubmit your design.</li></ul>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  |
| 106        | Degenerate nucleotides are included in the assay design region. For example, the W, R, S, N assay, or others.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   |
| 107        | Cannot locate the SNP sequence.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 |
| 108        | The final score is under assay limit.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           |
| 109        | The indels do not support the Infinium I assay type.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            |
| 110        | <p>The locus name is duplicated in the base commercial content.<br><br>Possible solution:</p><ul><li>Rename the locus name that is identified as duplicate in the excluded content file.</li></ul>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              |
| 111        | <p>The normalization bin count for the following species does not meet the minimum limit (100) required for ordering: <em>Homo sapiens.</em><br><br>Scenario:</p><ul><li>Any design that has normalization bin A/B that is > 0 and < 100, or a normalization bin C that is > 0 and < 1000.</li></ul><p>Possible solution:</p><ul><li>Remove or add \[G/C] and \[A/T] SNPs to within the limit.</li><li>Use the score.csv file to identify Bin A/B content and fill in a new Sequence Input file.</li><li>Replicate these designs, with unique names, to > 99.</li><li>Use the score.csv file to identify Bin C content. Redesign all Bin C using sequence input file, forcing Infinium I chemistry (Force\_Infinium\_to True), using unique names. Use the resulting score.csv file to fill Bin A/B to > 99. Combine content from multiple score files using the Existing Input file.</li></ul> |
| 112        | <p>The total bead count for this add-on does not meet the minimum limit {{MinBeadCount}} required for ordering.<br><br>Scenario:</p><ul><li>An Infinium iSelect design doesn't meet the required bead count limit for ordering.</li><li>An Infinium iSelect+ design does not meet the minimum bead count in the add-on content.</li></ul><p>Possible solution:</p><ul><li>Add more content or replicate the existing content using unique names.</li></ul>                                                                                                                                                                                                                                                                                                                                                                                                                                      |
| 113        | <p>The total bead count exceeds the maximum limit {{MaxBeadCount}} and cannot be ordered.<br><br>Scenario:</p><ul><li>A design exceeds the max bead count for ordering.</li></ul><p>Possible solution:</p><ul><li>Trim lower value content to below the limit.</li><li>Alternatively, contact Sales for additional options.</li></ul>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           |
| 114        | <p>The following species must occupy at least 20% of the total content for this design to be orderable: <em>Hordeum vulgare</em>.<br><br>Scenario:</p><ul><li>An Infinium XT iSelect design has a spewcies that does not occupy at least 20% of the total design.</li></ul><p>Possible solution:</p><ul><li>Add more content for the specified species or replicate the existing content using unique names.</li><li>Remove content from higher-represented species.</li></ul>                                                                                                                                                                                                                                                                                                                                                                                                                  |
| 115        | <p>The number of designed targets does not meet the minimum limit {MinimumTargetLimit}} required for ordering.<br><br>Scenario:</p><ul><li>An Infinium design does not meet the minimum target count for ordering.</li><li>An Infinium XT iSelect+ design does not have the minimum target count in the add-on content.</li></ul><p>Possible solution:</p><ul><li>Add more content or replicate the existing content using unique names.</li></ul>                                                                                                                                                                                                                                                                                                                                                                                                                                              |
| 116        | <p>The number of designed targets does not meet the maximum limit {MaxTargetDesignLimit}} required for ordering. Refer to the data sheet for the base content array and for the allowable add-on content.<br><br>Scenario:</p><ul><li>An Infinium design exceeds the maximum targets allowed for ordering.</li><li>An Infinium XT iSelect+ design's target count exceeds the maximum capacity.</li></ul><p>Possible solution:</p><ul><li>Trim lower value content to below the limit.</li><li>Alternatively, contact your Illumina sales representative for additional options.</li></ul>                                                                                                                                                                                                                                                                                                       |
| 117        | <p>The number of chromosomes exceeds the maximum allowed unique chromosomes per design. For example, 255.<br><br>Scenario:</p><ul><li>Any design exceeding 255 unique chromosomes will not proceed.</li></ul><p>Possible solution:</p><ul><li>Change chromosome fields to 0 until below the limit. Keep the look-up file as a reference during analysis.</li></ul>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              |
| 118        | <p>Representation of sex chromosome loci {sexrepresentation}% for normalization bin A {binA total count} exceeds limit of {RepresentationLimit}%.<br><br>Scenario:</p><ul><li>Any design with sex representation for Normalization Bins exceeding 20% of the total count for the bin will not proceed.</li></ul><p>Possible solution:</p><ul><li>Add non-sex chromosone content to Bin until below the limit. Or, remove sex chromosome content from Bin until below the limit.</li></ul>                                                                                                                                                                                                                                                                                                                                                                                                       |
| 301        | Polymorphism in duplicated region.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              |
| 302        | Melting temperature is outside assay limits.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |
| 304        | There are SNPs in the probe region. Refer to the Underlying\_SNP column for details.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            |
| 311        | SNP is not supported for Infinium I assay type.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 |
| 340        | Another polymorphism on the list is equal to or fewer than 60 nucleotides away.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 |
| 360        | <p>Low design score:<br><br>Possible solution:</p><ul><li>Remove the targets with a low design score and resubmit the targets for design.</li></ul>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             |
| 399        | Review the Score File or Input File used to create the design for inaccuracies.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 |
| 601        | The genome has multiple target sequences.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       |
| 602        | Probe sequence is duplicated in the base commercial content.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |
| 603        | <p>Probe sequence is duplicated in the custom content.<br><br>Possible solution:</p><ul><li>Remove the probes with duplicated sequence and resubmit the probes for design.</li></ul>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            |
| 604        | <p>The normalization bin count does not meet the recommended limit (200) for optimal performance if the species is a polyploid organism.<br><br>Secnario:</p><ul><li>Any polyploid design that has a normalization bin that falls between 100 and 200.</li></ul><p>Possible solution:</p><ul><li>Remove or add \[G/C] and \[A/T] SNPs to be within the limit.</li><li>Use the score.csv file to identify Bin A/B content and fill in a new Sequence Input file.</li><li>Replicate these designs, with unique names, to > 99.</li><li>Use the score.csv file to identify Bin C content. Redesign all Bin C using sequence input file, forcing Infinium I chemistry (Force\_Infinium\_I to True), using unique names. Use the resulting score.csv file to fill Bin A/B to > 99. Combine content from multiple score files using the Existing Input file.</li></ul>                                |

#### Methylation <a href="#methylation" id="methylation"></a>

| Error Code | Description                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           |
| ---------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| 101        | Flanking sequence is too short.                                                                                                                                                                                                                                                                                                                                                                                                                                                                       |
| 103        | <ul><li>Cannot determine the top/bot strand.</li><li>Low sequence complexity.</li></ul>                                                                                                                                                                                                                                                                                                                                                                                                               |
| 105        | <p>Polymorphism is on the mitochondrial genome. Illumina does not recommend using mitochondrial polymorphisms for oligo pools.<br><br>Possible solution:</p><ul><li>Remove any polymorphism on the mitochondrial DNA from your target file and resubmit your design.</li></ul>                                                                                                                                                                                                                        |
| 107        | Target Not found.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     |
| 108        | The final score is under assay limit.                                                                                                                                                                                                                                                                                                                                                                                                                                                                 |
| 115        | <p>The number of designed targets does not meet the minimum limit {MinimumTargetLimit}} required for ordering.<br><br>Scenario:</p><ul><li>An Infinium design does not meet the minimum target count for ordering.</li></ul><p>Possible solution:</p><ul><li>Add more content or replicate the existing content using unique names.</li></ul>                                                                                                                                                         |
| 116        | <p>The number of designed targets does not meet the maximum limit {MaxTargetDesignLimit}} required for ordering. Refer to the data sheet for the base content array and for the allowable add-on content.<br><br>Scenario:</p><ul><li>An Infinium design exceeds the maximum targets allowed for ordering.</li></ul><p>Possible solution:</p><ul><li>Trim lower value content to below the limit.</li><li>Alternatively, contact your Illumina sales representative for additional options.</li></ul> |
| 117        | <p>The number of chromosomes exceeds the maximum allowed unique chromosomes per design. For example, 255.<br><br>Scenario:</p><ul><li>Any design exceeding 255 unique chromosomes will not proceed.</li></ul><p>Possible solution:</p><ul><li>Change chromosome fields to 0 until below the limit. Keep the look-up file as a reference during analysis.</li></ul>                                                                                                                                    |
| 301        | Polymorphism in duplicated region. This means that a multi-mapper is found for this target. Hence, this target has been excluded.                                                                                                                                                                                                                                                                                                                                                                     |
| 399        | Review the Design File or Input File used to create the design for inaccuracies.                                                                                                                                                                                                                                                                                                                                                                                                                      |

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