BEGIN{# call with samtools view -F 4 r374c.bam  | awk -f /data/results/tools/ngs/sam/sam2aligned-fasta1.awk > r374.fa
#    $me = 10 ** (-$mQ / 10.0);
# Given 1000, for example, read alignments with mapping quality being 30, one of them will be wrong in average.
    FS="\t";
    print "MQ cutoff"th >"/dev/stderr";
}{
    id=$1;ref=$3;cig=$6;s=$10;mq=$5; o[mq]++;n++;
    if(i[id]>0){print "ERR "id" not uniq." >"/dev/stderr";}
    i[id]++;
    if (mq>=th){print ">"id,ref,cig,mq;print s;p++;}
}END{
    print "Passed "p" mappings  of "n"  "100.0*p/n" %" >"/dev/stderr";
    for (mq in o) {print mq" "100.0*o[mq]/n" "o[mq] >"/dev/stderr";}
 }