$re = '/NF.*?(\d*)\|.*/';
$str = 'NF3-9-16S_S9_1456|M02255:210:000000000-B9K3P:1:1101:14397:18152 1:N:0:9|o:50|m/o:0.720000|MR:n=0;r1=34;r2=2|Q30:p=97;p=100|CO:0|mismatches:36
NF3-9-16S_S9_9999|M02255:210:000000000-B9K3P:1:1101:14397:18152 1:N:0:9|o:50|m/o:0.720000|MR:n=0;r1=34;r2=2|Q30:p=97;p=100|CO:0|mismatches:36';
$subst = "Re1_91910_$1";
$result = preg_replace($re, $subst, $str);
echo "The result of the substitution is ".$result;
Please keep in mind that these code samples are automatically generated and are not guaranteed to work. If you find any syntax errors, feel free to submit a bug report. For a full regex reference for PHP, please visit: http://php.net/manual/en/ref.pcre.php