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MASCOT detected APPL1 in the muscle homogenate sample with sequence coverage of 56%.
For two species for which we received no voucher material or flowering and fruiting material for dissection, we verified proper identification of the sample with sequence comparison of vouchered data at loci always variable above the species level.
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Total InDel efficiency was then calculated using TIDE analysis (https://tide.nki.nl/ 24 comparing samples with sequence traces from untransfected cells.
Good quality COI barcode sequences were obtained for all 71 dried shark fin samples and 53 of the 58 dried gill plate samples, with sequence lengths varying between 93 and 664 bp (average length 508 bp).
Paired samples with sequence types that belonged to the same cluster were considered concordant infections, whereas paired samples with sequence types that belonged to different clusters were considered discordant infections.
aDiscordant multiple infections defined as: having ≥ 2 paired samples with sequence types that belonged to different clusters.
The data set was resampled down to the number of sequences found in the sample with fewest sequences (SSa_WoM_2; 2425 sequences) and the singletons were removed resulting in a total of 568 OTUs.
He compared the genetic sequences in those SIV samples with sequences from the few African green monkey SIV samples he had, as well as to sequences of human HIV-2 and macaque SIV.
Following the selection of each assay cut-off, assay sensitivity was evaluated using a total of 302 samples with sequence-detectable drug resistance mutations.
Since there are samples with sequences only for the NS5B region, the tMRCA was re-estimated using reduced data sets containing only NS5B sequences that had its E2 counterparts.
First, we were only able to collect two samples with sequencing data from both RNA libraries.
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