#!/usr/bin/perl

# http://perlmonks.org/?node_id=1137428

use strict;
use warnings;

$_ = <<END;
IMB,060410,V1 ,371094378,371096338,1961
IMB,060410,V1 ,371096340,371096486,147
IMB,107951,V1 ,981157588,981164939,7352
IMB,107951,V1 ,981164941,981165606,666
IMB,107951,V1 ,981165608,981175100,9493
IMB,107951,V1 ,981175102,981176199,1098
END

s/^(IMB,\d+,V1\s,)(\d+),\K
  (?:.*\n)+
  \1\d+,(\d+).*/$3/gmx;

print;