Supplemental Material for "Characterization of mutation spectra with ultra-deep pyrosequencing: application to HIV-1 drug resistance" by Wang et al.

Raw data:

The SFF format raw output from GS20 platform and the reference sequences can be found here.

Mapping results:

Using our newly developed asymmetric Smith-Waterman (ASW) algorithm, we mapped GS20 reads onto reference sequences, which were determined with conventional direct-PCR Sanger sequencing approach. Check here for mapping results.

In addition, we provided a web interface to pinpoint each variant detected by 454 platform by specifying a position of intererst. For the sample V11909, we sequenced 68 (31 1/100 cDNA dilution and 37 1/30 cDNA dilution) PCR products using Sanger approach to confirm minor variants revealed by the 454 platform. The confirmation results can be checked using the web interface by selecting species name 'V11909C'.

The colorful views of mapping results can be found here. Those files named *_na_orign.pdf show nucleotide variants before applying our filtering procedure and those named *_na_parsed.pdf show nucleotide variants after applying the filtering procedure. The amino acids variants files are named in a similar way. (Note in the amino acids variants map, synonymous varaints are merged together. Only the first 1kp sequence is shown in the nucleotide variants map.)

Contact Chunlin Wang if you need assistance using this site.