Methods, devices, and systems for analyte detection and analysis

A system for nucleic acid sample processing, comprising:

• a substrate comprising a first region and a second region different from said first region, wherein said first region or said second region comprises at least 10,000 indexed locations;
• a first source comprising a first set of nucleic acid molecules, wherein said first region of said substrate comprises a first set of indexed locations comprising nucleic acid molecules of said first set of nucleic acid molecules;
• a second source comprising a second set of nucleic acid molecules, wherein said second source is different than said first source, wherein said second region of said substrate comprises a second set of indexed locations comprising nucleic acid molecules of said second set of nucleic acid molecules;
• a detector configured to detect signals from said first set of indexed locations that are indicative of at least one nucleotide having been incorporated into a growing nucleic acid strand that is complementary to a nucleic acid molecule of said first set of nucleic acid molecules;
• and
• one or more processors, individually or in combination, configured to (i) receive said signals from said detector and (ii) associate each nucleic acid molecule of said first set of indexed locations with said first source or (iii) associate each nucleic acid molecule of said second set of indexed locations with said second source.