Genotyping-by-Sequencing allele frequency analysis Clause Samples

Genotyping-by-Sequencing allele frequency analysis. Sequenced fragments of DNA extracted from larvae and young-of-the-year (reference strata), generated during GBYP Phase 3, have been pooled into 5 separate populations: Gulf of Mexico (GOM), Eastern Mediterranean (EM, Levantine Sea), Central Mediterranean (CM, Strait of Sicily), Western Mediterranean (WMBA, Balearic Sea), Ligurian Sea (WMLI) and Tyrrhenian Sea (WMTY). All fragments were trimmed using a new algorithm with an improved capacity for trimming away excess nucleotides (barcodes and adaptors) in the sequenced fragments, allowing for better overlapping of reads. Forward and reverse sequence reads were overlapped and quality checked and filtered using FLASH tools (Table 5.1).
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