Soft-masking was used to avoid initial matches based on low complexity sequences and to allow extensions through masked regions.
It is reported in dbSNP at 0.7% based on low coverage sequence of ~600 individuals from the 1000 Genomes project (4 individuals).
We note that we excluded from this analysis cases where a given segment was misaligned due to a poor model prediction, predictions based on low quality sequence, and/or genomic gaps that affected protein prediction.
We introduce here the results obtained in high dimensional case (dimension higher than 20) and we point out the bad quality of the classical designs or the designs based on low discrepancy sequences but mainly the advantages of WSP designs.
This assumption is in accordance with results of a mitochondrial phylogeny suggesting a recent divergence of the genus Altolamprologus (Ernst, 2008) based on low levels of sequence divergence, frequently shared haplotypes and incomplete lineage sorting among A. compressiceps and A. calvus.
In three libraries, we encountered divergent Akkermansia sequences, based on low ANI values compared to the sequenced A. muciniphila genome.
We have shown that the sequence-based genotyping method can provide an ultra-high density genetic map of high quality SNPs, based on low-coverage sequences of a rice RIL population.
Recently, Spindel et al.[ 27] developed a custom-designed pipeline for SNP imputation, error correction, and streamlined data analysis based on low-coverage sequencing of a RIL population.
To prevent hits found based on low-complexity sequences or repeats the Sce_Assembly03 was masked using RepeatMasker [ 35] and the internal MIPS repeat database [ 36].
To advance this model system, we previously determined the first complete halobacterial genome sequence, that of H. sp. NRC-1 [ 2], In this present study, we analyzed the halophile family more broadly through a comparative genomic approach based on low-pass sequencing.
