I have a 1 kb amplicon sequenced on Ion Torrent platform that belongs to a virus. Statistics are given below
file virus_genome.fa data.fastq format FASTA FASTQ type DNA DNA num_seqs 1 60231 sum_len 9181 9416001 min_len 9181 25 avg_len 9181 156.3 max_len 9181 344
I have mapped those reads on to the virus genome using bwa with 88% mapping, but those reads only mapped to around 600-700 bps out of the entire genome. Look at below image from the IGV viewer.
I am wondering why there is no mapping covering the entire 1 kb amplicon; i.e. I am still missing ~ 400bps from my 1kb amplicon. Is it something to do with the wetlab or is it about the mapping (soft clipped bases somewhere) ?
Any help is much appreciated!