Marker density and read depth for genotyping populations using genotyping-by-sequencing.
Marker density and read depth for genotyping populations using genotyping-by-sequencing.
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DOI：
10.1534/genetics.112.147710
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发表时间：
2013-04
期刊：
影响因子：
3.3
通讯作者：
de Leon N
中科院分区：
文献类型：
--
作者：
Beissinger TM;Hirsch CN;Sekhon RS;Foerster JM;Johnson JM;Muttoni G;Vaillancourt B;Buell CR;Kaeppler SM;de Leon N
测序基因分型(GBS)方法提供低成本、高密度的基因信息。然而，GBS有独特的技术考虑因素，包括大量丢失的数据和序列读取的不均匀分布。这项研究的目的是用这种方法描述技术差异，并开发方法来优化阅读深度，以获得所需的标记覆盖率。为了经验性地评估利用GBS产生的片段的分布，在玉米参考近交系B73上产生了8.69 GB的GBS数据，利用∼进行基因组缩减和长度在75至81bp之间的单端阅读。我们观察到不同地点的序列覆盖率有很大的差异。大约76%的潜在可观察到的切割位点相邻序列片段没有测序读数，而有一部分具有比预期更大的读出深度，高达预期平均值的2369倍。本文中描述的方法有助于在经验性定义的读取深度的背景下确定测序深度，以达到遗传图谱研究所需的标记密度。
Genotyping-by-sequencing (GBS) approaches provide low-cost, high-density genotype information. However, GBS has unique technical considerations, including a substantial amount of missing data and a nonuniform distribution of sequence reads. The goal of this study was to characterize technical variation using this method and to develop methods to optimize read depth to obtain desired marker coverage. To empirically assess the distribution of fragments produced using GBS, ∼8.69 Gb of GBS data were generated on the Zea mays reference inbred B73, utilizing ApeKI for genome reduction and single-end reads between 75 and 81 bp in length. We observed wide variation in sequence coverage across sites. Approximately 76% of potentially observable cut site-adjacent sequence fragments had no sequencing reads whereas a portion had substantially greater read depth than expected, up to 2369 times the expected mean. The methods described in this article facilitate determination of sequencing depth in the context of empirically defined read depth to achieve desired marker density for genetic mapping studies.
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影响因子：
3.7
作者：
Baird NA;Etter PD;Atwood TS;Currey MC;Shiver AL;Lewis ZA;Selker EU;Cresko WA;Johnson EA
通讯作者：
Johnson EA
影响因子：
3.7
作者：
Baxter SW;Davey JW;Johnston JS;Shelton AM;Heckel DG;Jiggins CD;Blaxter ML
通讯作者：
Blaxter ML
影响因子：
64.8
作者：
通讯作者：
--
影响因子：
4.4
作者：
Chutimanitsakun Y;Nipper RW;Cuesta-Marcos A;Cistué L;Corey A;Filichkina T;Johnson EA;Hayes PM
通讯作者：
Hayes PM
影响因子：
3.3
作者：
Lough, Ashley N.;Roark, Leah M.;Newton, Kathleen J.
通讯作者：
Newton, Kathleen J.