{"id":1053,"date":"2026-02-09T20:36:18","date_gmt":"2026-02-10T02:36:18","guid":{"rendered":"https:\/\/open.qtlmax.com\/guide\/?p=1053"},"modified":"2026-02-12T10:26:15","modified_gmt":"2026-02-12T16:26:15","slug":"genome-browse","status":"publish","type":"post","link":"https:\/\/open.qtlmax.com\/guide\/index.php\/2026\/02\/09\/genome-browse\/","title":{"rendered":"Genome browse"},"content":{"rendered":"\n

This post explains how to perform the genome browsing in the proximity of quantitative trait loci (QTL) identified through genome wide associated studies (GWAS). Naturally, performing a GWAS is a prerequisite for using this feature. If you want to learn about the GWAS procedure, you can find a step-by-step guide here: https:\/\/open.qtlmax.com\/guide\/wp-admin\/post.php?post=302&action=edit<\/a><\/p>\n\n\n\n

Figure 1 shows the “Genome browse” tab in which a set of GWAS output files were selected, and all required configuration fields are filled out. <\/p>\n\n\n\n

The field labeled with “P cutoff” is for a P value threshold value to define QTL; the fields labeled with “Left margin (bp)” and “Right margin (bp)” define the window size by adding the left and right distances from a QTL marker (SNP). The combo box under the “Gbrowse servers” shows a list of gbrowse database servers. You can select a database upon a crop species you are working on. With all settings configured, pressing the [Execute] button will pop up a web browser as shown in Figure 2. Alongside with it, an item relevant to this work will be additionally listed as shown in Figure 1; each created item is clickable, allowing you to revisit the results later as needed. <\/p>\n\n\n\n

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

Figure 2 shows a web browser popped up, which displays a list of QTL markers that met the specified P-value threshold. Each record per QTL marker has a button. <\/p>\n\n\n\n

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

Clicking the button opens a new tab where you can view the genomic window on the genome browser server (Figure 3).<\/p>\n\n\n\n

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

QTLmax 6.0. further supports mapping QTL markers on chromosomes. To this end, you need to use Qmapper. On the right-bottom of the current QTLmax tab page, there is button called [Qmapper]. (Figure 4) <\/p>\n\n\n\n

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

If you press the [Qmapper] button, a new window form called “QTLmax Mapper” will pop up. (Figure 5) For more details, please visit here: https:\/\/open.qtlmax.com\/guide\/index.php\/2026\/02\/09\/physical-mapping-of-snps\/<\/a><\/p>\n\n\n\n

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

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

This post explains how to perform the genome browsing in the proximity of quantitative trait loci (QTL) identified through genome wide associated studies (GWAS). Naturally, performing a GWAS is a prerequisite for using this feature. If you want to learn about the GWAS procedure, you can find a step-by-step guide here: https:\/\/open.qtlmax.com\/guide\/wp-admin\/post.php?post=302&action=edit Figure 1 shows […]<\/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-1053","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\/1053","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=1053"}],"version-history":[{"count":25,"href":"https:\/\/open.qtlmax.com\/guide\/index.php\/wp-json\/wp\/v2\/posts\/1053\/revisions"}],"predecessor-version":[{"id":1366,"href":"https:\/\/open.qtlmax.com\/guide\/index.php\/wp-json\/wp\/v2\/posts\/1053\/revisions\/1366"}],"wp:attachment":[{"href":"https:\/\/open.qtlmax.com\/guide\/index.php\/wp-json\/wp\/v2\/media?parent=1053"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/open.qtlmax.com\/guide\/index.php\/wp-json\/wp\/v2\/categories?post=1053"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/open.qtlmax.com\/guide\/index.php\/wp-json\/wp\/v2\/tags?post=1053"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}