Methods and systems for determining sequencing read distances

A method for sequencing, comprising:

• (a) providing a nucleic acid molecule comprising a first region and a second region;
• (b) sequencing the first region by, in each flow step of a plurality of first flow cycles, incorporating a labeled nucleotide into a primer hybridized to the nucleic acid molecule and detecting the labeled nucleotide incorporated into the primer, or detecting a lack of incorporation thereof into the primer;
• and
• (c) determining distance information for the second region by, (i) in each flow step of a plurality of second flow cycles, providing a plurality of nucleotides to the primer, wherein, during the plurality of second flow cycles, one or more labeled nucleotides are incorporated into the primer, (ii) subsequent to at least two or more flow steps of the plurality of second flow cycles, detecting one or more signals from one or more labeled nucleotides incorporated into the primer, or detecting lack of incorporation thereof into the primer, without detecting the one or more signals from the one or more labeled nucleotides incorporated into the primer, or the lack of incorporation thereof, between at least two or more flow steps in the plurality of second flow cycles, and (iii) determining distance information indicative of a length of the second region based at least in part on a relationship between an intensity of the one or more signals and a distance.