Sentence examples for low depth sequencing from inspiring English sources

In rice, the most important crop plant in terms of human consumption, this is exemplified by the development of SNP genotyping platforms (Zhao et al. 2011), low depth sequencing for genome wide association mapping (Huang et al. 2010) and now deeper sequencing of large collections (3K RGP 2014).

Mis-assemblies and gaps usually result from repeats as well as secondary structures, either in unrepresented GC-rich regions or in un-sequenced regions due to a low depth sequence coverage [ 34].

This problem dramatically increases at low-depth sequencing.

The genotypic markers were derived from low-depth sequencing with 78% missing data on average.

The third advantage is that the VB method can accurately detect recombination blocks even with low-depth sequencing data.

Thus, low-depth sequencing provides mostly new sequence and avoids the high redundancy seen in large-scale genome projects.

Resequencing analyses of major crop plants, including soybean, rice, and maize, using a low-depth sequencing coverage have been reported recently.

This approach, where positions that were not genotyped in the sample are added using phase information in the reference set, is also relevant to refining genotype calls for low-depth sequencing data.

However, due to the low-depth sequencing of toxin transcripts for each species, fast evolution of toxin genes, and lack of genome sequences, the detailed elaboration of snake venom evolution is still unclear.

Single nucleotide variations (SNVs) and insertion and deletion (indels) were called from pileup files using SNooPer, an in-house variant caller that is based on a machine learning approach and developed to minimize false positive variant calling in low-depth sequencing data (manuscript submitted and software available upon request).

These missing data and false negatives resulted from library construction, the relatively low depth of sequencing coverage per progeny individual due to multiplexing, and sequencing biases created by the sequencing platform employed in this investigation, following initial marker ordering.