BWA-MEM also has better performance than BWA-backtrack for 70-100bp Illumina reads.For 70bp or longer Illumina, 454, Ion Torrent and Sanger reads, assembly contigs and BAC sequences, BWA-MEM is usually the preferred algorithm. BWA-SW may have better sensitivity when alignment gaps are frequent. Multi-part alignments are possible in the presence of structural variations, gene fusion or reference misassembly.
A translator for the flags can be found here explain-flags. You also see that the first read has a mapping quality of 0 (this is phred-scale) and the "cigar" is "100M". You can see the sequence of the read and the qualities as well.The fact that is have mapping quality 0 means that the probability that the read was mapped wrong is 1!Note that for Illumina reads, bwa-backtrack may optionally trim low-quality bases from the 3'-end before alignment and thus is able to align more reads with high error rate in the tail, which is typical to Illumina data.BWA-SW and BWA-MEM both tolerate more errors given longer alignment.The first algorithm is designed for Illumina sequence reads up to 100bp, while the rest two for longer sequences ranged from 70bp to 1Mbp.
BWA-MEM and BWA-SW share similar features such as long-read support and split alignment, but BWA-MEM, which is the latest, is generally recommended for high-quality queries as it is faster and more accurate.Internally BWA concatenates all reference sequences into one long sequence.A read may be mapped to the junction of two adjacent reference sequences.mapped) can be achieved by -F 4: We can also filter on the mapping quality, eg.getting all reads with a mapping quality larger than eg 30, will remove the unmapped/multi-mapped reads (mapping quality 0) and the read mapped with mapping quality 10. You can also see the flags have changed, now it also contains information on pairing, whether the paired read was mapped etc.For the alignment the fields are: Read name, flag, reference it mapped to, position, mapping quality, cigar, mate reference map, mate position, template length, read sequence and read qualities. You should see that the first read is mapped to chr21 at around 5.1Mb.