Sequencing error simulations

Sequencing errors of substitutions and indels (insertions and deletions) were introduced to reads of uniformly 350 bp simulated from Populus trichocarpa chromosomes 1–19 (v3.0, DOE-JGI, http://www.phytozome.net/poplar) at 0.1x coverage using Grinder v0.5.3. In terms of sequencing error type, simulations included substitution-biased (substitutions/indels ratio of 90:10) and indel-biased (substitutions/indels ratio of 10:90) sequencing errors. In terms of sequencing error rate distribution, we assumed that sequencing errors occurred either uniformly or linearly from the 5′ end to 3′ end of each read. With uniformly distributed sequencing errors, reads were simulated with an error rate of 0, 0.01%, 0.1%, 0.5%, 1%, 2%, 3%, and 5%. With linearly distributed errors, the error rate doubled from the 5′ end to 3′ end: 0, 0.01–0.02%, 0.1–0.2%, 0.2–0.4%, 0.5–1%, 1–2%, and 2–4%. For the file name of each simulation, the first three letters reflect the error rate distribution (e.g. Lin for linear error rate distribution, Uni for uniform distribution); the following 4 digits represent the sequencing error type (e.g. 9010 for substitutions/indels ratio of 90:10); the remaining digits indicate the error rate (e.g. 0.1%). When error rate was 0, the simulation was designated as ErrorRate_0.