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!
Three extra columns are now filled, where the "=" means that the pair mapped to the same chromosome, then the mapping position of the pair and the distance between the pairs (the size of the entire DNA fragment). read unmapped=4, mate unmapped=8, to get the reads that are both unmapped and that the mate is unmapped: 4 8=12 Lets try some reads from a study of Pseudomonas aeruginosa, an opportunistic pathogen that can live in the environment and may infect humans.Note down the time for each command, it is the third number that is written, something like m:First go to your work dir, create a folder for the exercise and copy data to there (I wrote down all the commands, but you probably know how to do you).However, representing multi-part alignments in SAM has not been finalized.To make BWA work with your tools, please use option `-M' to flag extra hits as secondary.
Bwa single end reads
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.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.Bwa-back is mainly designed for sequencing error rates below 2%.