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However, the randomness associated with sampling multiple reads in heterozygotes and the inherent error in base calling and alignment makes calling genotype based on less extreme observations ambiguous.
All sequences were compiled from multiple reads in both directions and line-ups and annotations were carried out using Contig express and Vector NTI.
Compression of library data was achieved by annotating the frequency of each unique sequence into its respective identifier, thereby removing multiple reads in FASTA format.
The number of genes does not equal the summation of gene components because there are some genes that are hit by multiple reads in different sections of the gene.
Similar(56)
Of the 155 SNPs that appeared in multiple reads, 66 occurred in different fish (libraries).
When read counts are extremely high, as in the case of Rubisco, sequencing errors occur in multiple reads which are then assembled into separate, artifactual contigs.
As a matter of fact, variability could be introduced by 454-sequencing [ 39] and PCR amplification; in particular, errors produced in the early PCR cycles could then be spread in multiple reads with a low possibility to distinguish them from real SNCs.
This is because plasma DNA fragments, whose paired-end reads map to different chromosomes or to the same chromosome but at large distances (several kb) apart, will likely not be detected in multiple reads.
Although the use of an initial data quality check and reads filtering step eliminates a great amount of them, a potentially large number of artefacts is still expected to remain, including many present in multiple copies within amplicons (in our study: total number of filtered reads: 63,166; artefacts: 33,400; artefacts occurring in multiple reads: 11,685,=18.2% of the filtered reads, Figure 2).
Although the estimated level of misassignment was about two times higher than reported previously [ 40, 47], it was still low enough to ensure that misassigned reads are rare, and as such will not affect the outcome of genotyping, which requires an allele to be present in multiple reads.
In addition, multiple reads matched to uncharacterized positions on 59 different primary miRNA sequences.
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