I can't seem to figure out why 0% is mapped. The bam file was obtained after aligning paired-end fastq files against my custom fasta reference file using 'bwa mem'.
samtools flagstat sample.bam
51174 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 duplicates
0 + 0 mapped (0.00%:nan%)
51174 + 0 paired in sequencing
25587 + 0 read1
25587 + 0 read2
0 + 0 properly paired (0.00%:nan%)
0 + 0 with itself and mate mapped
0 + 0 singletons (0.00%:nan%)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)
Any pointers will be much appreciated. Thanks!
samtools flagstat sample.bam
51174 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 duplicates
0 + 0 mapped (0.00%:nan%)
51174 + 0 paired in sequencing
25587 + 0 read1
25587 + 0 read2
0 + 0 properly paired (0.00%:nan%)
0 + 0 with itself and mate mapped
0 + 0 singletons (0.00%:nan%)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)
Any pointers will be much appreciated. Thanks!
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