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On average, 58.3% of sequenced reads could be mapped to unique locations in the A. queenslandica genome (19 45 million mapped reads).
A total of 4,272 SNPs could be mapped to unique locations evenly distributed over the chicken genome.
As no sophisticated normalization method was explored, most detected interactors cannot be mapped to unique UniProtKB IDs.
From wt cells, we obtained 14,358,325 reads, of which 9,771,440 (68.1%) could be mapped to unique positions in the genome.
We ignored the probesets such as '_f_at', '_s_at' and '_x_at' because they could not be mapped to unique genes in a gene family.
Among all the DNA fragments detected in each sample, we selected only those with high sequencing and matching quality that could be mapped to unique genomic locus.
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The vast majority of all reads were mapped to unique positions except a very small percentage (1.69-3.09%).
Among the aligned reads, approximately 86% and 65% were mapped to unique genomic regions in muscle and adipose tissues, respectively.
Differentially expressed genes were mapped to unique promoters and the TF binding sites were analyzed in PAINT using TRANSFAC® Profession 10.1 database and associated MATCH® tool [ 59].
Among these probes, 233 probes were mapped to unique Entrez Gene IDs, 7 probes were mapped to more than one Entrez Gene IDs, and 14 probes were not mapped, respectively.
Read mapping to the chicken reference sequence (WUGSC 2.1/galGal 3) was conducted using BWA (Li and Durbin 2010), and 85.70% and 74.83% of the input reads were mapped to unique positions on the chicken reference genome for Silkie and L2, respectively.
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