0001140361-23-011185 Sample Contracts

INDENTURE Dated as of [•], 20__ Debt Securities
Bionano Genomics, Inc. • March 10th, 2023 • Laboratory analytical instruments • New York

Indenture, dated as of [•], 20__, among Bionano Genomics, Inc., a Delaware corporation (the “Company”), and [Trustee], as trustee (the “Trustee”):

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BIONANO GENOMICS, INC. and , AS WARRANT AGENT FORM OF DEBT SECURITIES WARRANT AGREEMENT DATED AS OF [ ], 20
Debt Securities Warrant Agreement • March 10th, 2023 • Bionano Genomics, Inc. • Laboratory analytical instruments • New York

This DEBT SECURITIES WARRANT AGREEMENT (this “Agreement”), dated as of between BIONANO GENOMICS, INC., a Delaware corporation (the “Company”), and , a [corporation] [national banking association] organized and existing under the laws of and having a corporate trust office in , as warrant agent (the “Warrant Agent”).

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BIONANO GENOMICS, INC. and , AS WARRANT AGENT FORM OF COMMON STOCK WARRANT AGREEMENT DATED AS OF [ ], 20
Common Stock Warrant Agreement • March 10th, 2023 • Bionano Genomics, Inc. • Laboratory analytical instruments • New York

This COMMON STOCK WARRANT AGREEMENT (this “Agreement”), dated as of between BIONANO GENOMICS, INC., a Delaware corporation (the “Company”), and , a [corporation] [national banking association] organized and existing under the laws of and having a corporate trust office in , as warrant agent (the “Warrant Agent”).

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BIONANO GENOMICS, INC. and , AS WARRANT AGENT FORM OF PREFERRED STOCK WARRANT AGREEMENT DATED AS OF [ ], 20
Preferred Stock Warrant Agreement • March 10th, 2023 • Bionano Genomics, Inc. • Laboratory analytical instruments • New York

This PREFERRED STOCK WARRANT AGREEMENT (this “Agreement”), dated as of between BIONANO GENOMICS, INC., a Delaware corporation (the “Company”), and , a [corporation] [national banking association] organized and existing under the laws of and having a corporate trust office in , as warrant agent (the “Warrant Agent”).

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AMENDMENT NO. 1 TO SALES AGREEMENT March 9, 2023
Sales Agreement • March 10th, 2023 • Bionano Genomics, Inc. • Laboratory analytical instruments

This Amendment No. 1 (“Amendment No. 1”) amends that certain Sales Agreement, dated as of March 23, 2021 (the “Agreement”), by and between Bionano Genomics, Inc. (the “Company”) and Cowen and Company, LLC, as sales agent (the “Agent”). Defined terms used herein and not otherwise defined shall have the meaning assigned to such terms in the Agreement.

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