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This was confirmed to be a splice form (which we call CG6995-R-D CG6995-R-D CG6995-R-D frame and thatslates to a pretainslacking the readingain (CG6995-P-D) with a predicted, unmodiframemand of 63 kiloDaltranslatesI of 5.22.
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The original Hi-C method only retains read pairs in which both reads map completely to the reference genome.
Also, the mean GC content is higher for motifs that retain reading frame, and this accords with a higher GC content within coding sequence than elsewhere.
Furthermore, the reads of D4* have been quality filtered, so that we only retained reads in which all bases have a high quality score.
We therefore chose a bit-score cut-off of 250, which, although still retaining reads with less than 97% identity, was determined as the best threshold by virtue of retaining the majority of true positive hits, while maintaining a minimum number of true negatives.
The expected Ves sequence was identifiable in 99.6 99.8% of Ves reads from all retained read pairs.
We only retained reads that mapped uniquely, but allowed up to two mismatches.
Retained reads were sorted into loci and genotyped using Stacks software 0.9995 [ 25].
We only retained reads that did not contain adapters, determined by a BLAST search.
Retained reads were demultiplexed and trimmed to 94 bp by removing the barcode and terminal base.
All retained reads were output in SAM format for further analysis.
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