This is my pipeline for the human reads to map with human reference: (I use default solid2fastq.pl script which is in BWA package)
#! /bin/bash -l
#index the reference
bwa index -a bwtsw human_g1k_v37.fasta &&
#aligne the file with reference
bwa aln human_g1k_v37.fasta Read.single.fastq > Read_out.sai &&
#Convert the alignment output to a SAM file
bwa samse human_g1k_v37.fasta Read_out.sai Read.single.fastq > Read_out.sam &&
#extract the unmapped reads
awk '{if (substr($1,1,1)=="@") {print $0} else {if ($3!="*") {print $0}}}' Read_out.sam > out.sam
#convert to BAM file
samtools view -b -S Read_out.sam > Read_out.bam &&
#sort the BAM file
samtools sort Read_out.bam Read_out.bam.sorted &&
#index the BAM file
samtools index Read_out.bam.sorted.bam &&
#Delete redundant reads/duplicates
samtools rmdup Read_out.bam.sorted.bam Read_out_final.bam.sorted.bam &&
#computing Mapping Quality
samtools view Read_out_final.bam.sorted.bam -f human_g1k_v37.fasta | awk '{x+=$5}END{print x/NR}' > MAPQ.txt&&
But only 54,538 reads mapped with human reference and the mapped quality is 0.00140495 . I don't know what's wrong in pipeline to got this mapped quality.
Thanks for your explanation.
This is fastqc output