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.本数据集采用Grinder v0.5.3软件，对从毛果杨（Populus trichocarpa）1至19号染色体（v3.0版本，DOE-JGI，http://www.phytozome.net/poplar）模拟得到的长度统一为350 bp的测序读段（reads），以0.1x覆盖度引入碱基替换与插入缺失（insertions and deletions，indels）类测序错误。 按测序错误类型划分，模拟包含两类错误模式：替换偏好型（碱基替换与插入缺失比例为90:10）与插入缺失偏好型（碱基替换与插入缺失比例为10:90）。 在测序错误率分布维度，本数据集模拟了两种分布形式：均匀分布与从测序读段5'端到3'端线性递增分布。 对于采用均匀分布的测序错误，模拟设置的错误率分别为0、0.01%、0.1%、0.5%、1%、2%、3%及5%。 对于采用线性分布的测序错误，错误率从5'端到3'端呈翻倍增长，对应错误率区间依次为0、0.01–0.02%、0.1–0.2%、0.2–0.4%、0.5–1%、1–2%及2–4%。 各模拟数据集的文件名命名规则如下：前三位字母代表错误率分布类型（例如Lin代表线性分布，Uni代表均匀分布）；后续四位数字代表测序错误类型（例如9010代表碱基替换与插入缺失比例为90:10）；剩余数字则表示测序错误率（例如0.1%）。 当测序错误率为0时，该模拟数据集命名为ErrorRate_0。