I see over and over again templates and suggestions about what to include in a query. For instance, Carissa Taylor posted an excellent blog on pitch as story, including a template and links to other templates (all of which are helpful!). In addition to the pitch, a query can have comp titles and a biography (although whether they are necessary varies on the agent). There is plenty of information on what to include in a query.
But your novel is most likely between 50,000 and 100,000 words. That means a LOT will be left out. What exactly should that be?
As Taylor notes in her post, your novel probably has several moments that could be used as the final moment of decision, from the first plot point way up to the final climax. Which one you choose, Taylor says, should be a matter of which one is the most exciting. Another factor to consider is which one is easier to condense.
Novels are complicated creatures by design. Subplots should roll into the main plot for a satisfying conclusion, where something seemingly unrelated becomes the cornerstone, or the subplots and main plot echo each other in a thematically resonant way. By necessity, this can't all fit into your query.
So, what exactly do you leave out?
First, the logline. With few exceptions, if the first sentence of your query could be read in Movie Trailer Voice (you know the one), it can be deleted and it probably should be. Queries don't need to start with anything along the lines of, "For star-crossed lovers Qui-gon Jinn and Jar Jar Binks, the only thing separating them is 17,000 light years and parents who hate each other." or "Love. Loss. Growing up. In this epic tale of forgiveness and bittersweet romance..."
Instead, start with the characters themselves. Let the words of the plot and characters tell us about your theme instead of spelling it out.
Second, almost every single subplot. A general rule of thumb is not to name more than three characters in a query: the protagonist, the antagonist, and a sidekick or romantic interest. I fought this tooth and nail with the second book I queried. I was certain I needed the three above AND two more characters. I cut it down to three named and one mentioned but unnamed, and while I wasn't happy about it, I know my query was better for it.
Even when I receive the go-ahead on my queries from my critique partners, I usually find them woefully inadequate. But when I read queries for stories I haven't read yet, the effective ones get me excited to read the rest, and pleasantly surprised when the story turns out to be even more complicated and interesting than I had thought based on the query alone.
Instead, focus on a through-line that makes sense. Don't get distracted by details that don't relate to the main plotline. Additionally, keep in mind the third point.
The third thing you can leave out is the whole truth. I hate to be the one who breaks this to you, but queries sometimes lie. When you leave out subplots and characters, the way that something actually happens likely isn't exactly the way you're going to describe it. There is a fine line between including every detail of an intricate plot and only saying "One thing leads to another," but it's okay if that line doesn't say something exactly. If it's a minor character who shows your protagonist the key to solving her dilemma, you aren't going to introduce the minor character for just that moment.
Instead, use passive voice. I know. I'm crazy. But when it comes to simplifying things without being too vague, it can work. Instead of "The protagonist gives up and sits down for a meal at her favorite diner. To her surprise, the waitress mentions a hidden trail near the top of Mt. Hood that is just the clue the protagonist needed to set out toward the third act." Write, "When the location of the hidden trail is revealed, it's the final clue she needs. But at the top is a fork in the road and she must choose: go up and chance running into Bigfoot, or go around and risk the landslides that have been plaguing the mountain." This gets us to the important part--the choice she has to make--without bogging us down in too many details (Although the rough draft example I provided probably still has too many details.)
Finally, irrelevant biographical information. Unless an agent specifically asks for it, your biography can be nonexistent.
Instead, any information in your biography should be directly relevant to writing and/or the subject of your book. If you have an MFA or are working toward one, say so. No need to mention your five pet dogs or the amount of time you spend on Tumblr. However, if your character is a web designer and you spent ten years in the business, that's something relevant you can include.
What things are you tempted to include in your query that would be best left unsaid?