Query Type	Instruction
Gene	There are three main ways of querying genes: Exact gene symbol Gene symbols starting with a certain term followed by a *. A list of gene symbols delimited by a comma. Examples: Entering CHD8 would pull up all CHD8 variants. Entering CHD* would pull up every gene starting with CHD (CHD1, CHD1L, CHD2, ..., CHDH) Entering CHD8, MECP2, PAX4 would give all variants in these 3 genes
Chr. Position	This allows for you to search for variants based on their chromosome and position location. Examples: chr14:21,806,838-21,946,382 chr14:21806838-21946382 14:21806838-21946382 chr14:21,871,373 chr14:21871373 14:21871373 14:21,871,373
Phenotype	The database can be searched by the phenotype of interest. Just start to type the word you are interested in and denovo-db will give you a list of phenotypes in the database that match your input. For example, entering de, you get the following phenotypes to choose: developmental_disorder neural_tube_defects
Function	Variants can be searched by their functional annotation. Start typing the functional category you are interested in and denovo-db will give you the options. For example, typing sp, you get the following function classes to choose, splice-acceptor splice-donor
CADD Threshold	This query sets the minimum CADD score threshold you want to view. For instance if you type 40 it will list all variants with a CADD >= 40 in the database.
Sample ID	This query is often most useful when you've already done a different search and you want to see what other variants a sample might want to have. For example, you search for mutations in CHD8 using the gene query. You find that sample 11654.p1 has a splice-acceptor mutation and than want to know what else that sample has so you go to the sample query and type in 11654.p1 in the search. This shows you that this sample has 3 validated de novo mutations in RERE, CHD8, and GNPDA1, respectively.
Study	This allows you to type in a study name and search only by that study. Just start to type the word you are interested in and denovo-db will give you the options. For example, typing AS, you get the following studies to choose, Dimassi2015 Hashimoto2015 Tavassoli2014

Other features included,

• 1. Filtering variants. Type in any term in the "Filter" field on the top left side above the table, the variant table will display entries matching your term. For example, enter missense, only missense variants within the current queried result will be displayed in the table.
• 2. Sorting columns. Each column can be sorted ascending or descending by clicking the arrows in the column headers.
• 3. Selecting columns. Select columns to show or hide using the "Show / hide columns" button on the top right side above the table.
• 4. Selecting table size per page. Select number of entries to display per page using "Show entries" pull-down menu on the top right side above the table.
• 5. Exporting data. The full queried data set can be exported to a tab-separated-value (TSV) file through the "Export to TSV" button on the top right side above the table. The output .tsv file may contain more entries than what is displayed online without filtering, and may contain all annotated entries due to alternative transcripts. It also contains more attributes than what are displayed online.