{"id":1055,"date":"2026-02-09T20:37:59","date_gmt":"2026-02-10T02:37:59","guid":{"rendered":"https:\/\/open.qtlmax.com\/guide\/?p=1055"},"modified":"2026-02-20T03:33:49","modified_gmt":"2026-02-20T09:33:49","slug":"physical-mapping-of-snps","status":"publish","type":"post","link":"https:\/\/open.qtlmax.com\/guide\/index.php\/2026\/02\/09\/physical-mapping-of-snps\/","title":{"rendered":"Qmapper: Tool for physical mapping with SNPs"},"content":{"rendered":"\n

This post explains how to visualize a physical map of SNPs. Simply put, this physical map is a graphical representation, so called an ideogram. However, QTLmax offers functionality far beyond other ideogram tools:<\/p>\n\n\n\n

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  1. Interactive Markers:<\/strong> Marker names are clickable and link directly to the designated genomic <\/strong>region in a genome browser.<\/li>\n\n\n\n
  2. Integrated Layout:<\/strong> Physical chromosome maps can be aligned with corresponding Manhattan plots in the top and bottom spaces. This provides a more intuitive comparison between a marker’s physical position and its QTL signal.<\/li>\n\n\n\n
  3. Advanced Customization:<\/strong> The design of the physical map can be finely tuned through a wide range of flexible editing options.<\/li>\n<\/ol>\n\n\n\n

    The tool for these graphics is called Qmapper<\/strong>, which was first introduced with the launch of QTLmax 5.0.
    From now on, let’s get started with how to construct a physical map of SNPs using QTLmax 6.0. For your brief overview, Figure 1 is a resulting output as an example; we are going to make the exact output in this tutorial.<\/p>\n\n\n\n

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    (Figure 1)<\/p>\n\n\n\n

    “Qmapper is a dedicated application. You can launch it by clicking the [Qmapper] button (highlighted with a red square) located at the bottom-right of the ‘Genome browse’ tab, or by selecting the ‘Qmapper’ item under the Mapper menu at the top (Figure 2).”<\/p>\n\n\n\n

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    (Figure 2)<\/p>\n\n\n\n

    Shown in Figure 3 is the appearance of Qmapper. In order to display a layout of chromosomes for template of SNPs, you must load a chromosome-template file which is in a text format. <\/p>\n\n\n\n

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    (Figure 3)<\/p>\n\n\n\n

    The text file for chromosome template can be found in the following path:<\/p>\n\n\n\n

    ~\/Documents\/QTLmax\/demo\/mapper\/rice_genome.txt<\/strong><\/p>\n\n\n\n

    Figure 4 showcases its contents, which include each chromosome number and its total length. In each record, the two values can be separated by either spaces or tabs. Clicking the [Load Chromosomes] button opens a file browser, allowing you to select the template file. In this tutorial, the above file was selected from at the designated path.<\/p>\n\n\n

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    \"\"<\/figure>\n<\/div>\n\n\n

    (Figure 4)<\/p>\n\n\n\n

    Figure 5 shows the Qmapper interface after the chromosome template has been drawn. You can see a list of records is shown in the central panel.<\/p>\n\n\n\n

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    (Figure 5)<\/p>\n\n\n\n

    Next, let us add SNP markers to be positioned on the template. Pressing the [Add\/Remove markers] button will pop up a new form as shown in Figure 6.<\/p>\n\n\n\n

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    (Figure 6)<\/p>\n\n\n\n

    Make sure to enter a trait name in association with the SNPs to visualize. After that, pressing the [Select a corresponding HTML] button opens a file browser, allowing you to select an HTML file; please note that the HTML file must be an output generated by ‘Genome browse’ feature in QTLmax 6.0. (See Figure 7)<\/p>\n\n\n\n

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    (Figure 7)<\/p>\n\n\n\n

    Figure 8 showcases the interface of the popup window after confirming the selection of an HTML file you desire. <\/p>\n\n\n\n

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    (Figure 8)<\/p>\n\n\n\n

    Pressing the [Confirm] button will lead to the interface shown in Figure 9. The bottom panel is filled with new information related to the SNPs fed from the input dataset. <\/p>\n\n\n\n

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    (Figure 9) <\/p>\n\n\n\n

    Pressing the [Draw Chromosomes] button will make the SNPs appear on the top panel as shown in Figure 10. It is important to note that each marker name is clickable, linking directly to a genomic window encompassing the respective SNP. Each window range is pre-defined by the ‘Genome browse’ feature in QTLmax 6.0. (For more details, visit here: https:\/\/open.qtlmax.com\/guide\/index.php\/2026\/02\/09\/genome-browse\/<\/a>)<\/p>\n\n\n\n

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    (Figure 10)<\/p>\n\n\n\n

    Clicking each SNP name will open up a new web browser, leading to its genome browse window. (Figure 11)<\/p>\n\n\n\n

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    (Figure 11)<\/p>\n\n\n\n

    Sometimes you may want to hide some SNPs from the visualized map. If it is the case, pressing the [Marker filter] button will pop up a new form as shown; therein, you can send SNP names to hide to the panel on the right hand side. (Figure 12)<\/p>\n\n\n\n

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    (Figure 12)
    Pressing the [Draw chromosomes] button will lead to updating the physical map in the map display panel as shown in Figure 13. <\/p>\n\n\n\n

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    (Figure 13)<\/p>\n\n\n\n

    If you want to adjust the figure’s appearance, select ‘Template Panel’ from the ‘Template’ menu on the top bar. A new window will appear featuring nine horizontal sliders and two check boxes (Figure 14).<\/p>\n\n\n

    \n
    \"\"<\/figure>\n<\/div>\n\n\n

    (Figure 14)<\/p>\n\n\n\n

    To change the chromosome color, select ‘Chromosome color’ from the ‘Template’ menu on the top bar. A color palette window will then appear (Figure 15).<\/p>\n\n\n

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    \"\"<\/figure>\n<\/div>\n\n\n

    (Figure 15)<\/p>\n\n\n\n

    Figure 16 displays the updated physical map with the new graphical settings applied. <\/p>\n\n\n\n

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    (Figure 16)<\/p>\n\n\n\n

    So far, we have represented a list of SNPs in the chromosome panel. From now on, this tutorial will show how to create a Manhattan plot, so that the same SNPs will be outstanding in a different graphical way. To do this, you must load the ‘pvalues_map.csv’ file by pressing the ‘Add\/Remove Manhattan’ button. Pressing the button will pop up a new window for loading ‘pvalues_map.csv’ as an input file (Figure 17); it is important to note that the input file is automatically created as a result of GWAS procedure in QTLmax 6.0. <\/p>\n\n\n\n

    In this example, since the visualized SNPs were named ‘M1’ as their associated trait name (Figure 7), it is logical to enter the same name in the ‘<\/strong>Trait name‘<\/strong> box. Next, clicking the [Select a corresponding CSV] button will open a file browser, allowing you to select the ‘pvalue_map.csv’ file of interest. (Figure 17)<\/p>\n\n\n\n

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    \"\"<\/figure>\n<\/figure>\n\n\n\n

    (Figure 17)<\/p>\n\n\n\n

    Figure 18 shows the interface after the input file has been chosen. <\/p>\n\n\n\n

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    (Figure 18)<\/p>\n\n\n\n

    Clicking the [Confirm] button will display the interface shown in Figure 19, where the new Manhattan plot is visible under the newly created ‘M1’ tab. (Figure 19)<\/p>\n\n\n\n

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    (Figure 19)<\/p>\n\n\n\n

    You can add a P-value threshold line by entering a desired threshold number, followed by pressing the [Apply] button. (Figure 20)<\/p>\n\n\n\n

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    (Figure 20)<\/p>\n\n\n\n

    If you want to see information about each SNP in detail, press the [Red marker list] button; then a new pop-up window will show a list of SNP information as shown in Figure 21. <\/p>\n\n\n\n

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    (Figure 21)<\/p>\n\n\n\n

    Essentially, a Manhattan plot figure resulting from a GWAS procedure can be exported to an image file by using QTLmax Workbench in a sophisticated manner. <\/p>\n\n\n\n

    Similarly, the resulting SNP physical map can also be exported to an image file. To this end, select ‘Map viewer’ from the ‘Template’ menu on the top bar; a new image window will appear displaying the image as shown in Figure 22. Note that the SNP labels in this window is not clickable. <\/p>\n\n\n\n

    You can adjust the image position within the panel using two sliders at the bottom, labeled ‘Horizontal margin’ and ‘Vertical margin.’ Once the image is positioned as desired, pressing the [Save the image button] will create the resulting image file at the designated path in green text on top of the image panel. (Figure 22) <\/p>\n\n\n\n

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    (Figure 22)<\/p>\n\n\n\n

    <\/p>\n","protected":false},"excerpt":{"rendered":"

    This post explains how to visualize a physical map of SNPs. Simply put, this physical map is a graphical representation, so called an ideogram. However, QTLmax offers functionality far beyond other ideogram tools: The tool for these graphics is called Qmapper, which was first introduced with the launch of QTLmax 5.0.From now on, let’s get […]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_bbp_topic_count":0,"_bbp_reply_count":0,"_bbp_total_topic_count":0,"_bbp_total_reply_count":0,"_bbp_voice_count":0,"_bbp_anonymous_reply_count":0,"_bbp_topic_count_hidden":0,"_bbp_reply_count_hidden":0,"_bbp_forum_subforum_count":0,"footnotes":""},"categories":[1],"tags":[],"class_list":["post-1055","post","type-post","status-publish","format-standard","hentry","category-guide"],"_links":{"self":[{"href":"https:\/\/open.qtlmax.com\/guide\/index.php\/wp-json\/wp\/v2\/posts\/1055","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/open.qtlmax.com\/guide\/index.php\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/open.qtlmax.com\/guide\/index.php\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/open.qtlmax.com\/guide\/index.php\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/open.qtlmax.com\/guide\/index.php\/wp-json\/wp\/v2\/comments?post=1055"}],"version-history":[{"count":75,"href":"https:\/\/open.qtlmax.com\/guide\/index.php\/wp-json\/wp\/v2\/posts\/1055\/revisions"}],"predecessor-version":[{"id":1649,"href":"https:\/\/open.qtlmax.com\/guide\/index.php\/wp-json\/wp\/v2\/posts\/1055\/revisions\/1649"}],"wp:attachment":[{"href":"https:\/\/open.qtlmax.com\/guide\/index.php\/wp-json\/wp\/v2\/media?parent=1055"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/open.qtlmax.com\/guide\/index.php\/wp-json\/wp\/v2\/categories?post=1055"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/open.qtlmax.com\/guide\/index.php\/wp-json\/wp\/v2\/tags?post=1055"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}