S2 S1 S3 S4 S5
G1 11 12 13 14 15
G2 21 22 23 24 25
G3 31 32 33 34 35
G4 41 42 43 44 45

Sample Loc Rep T1 T2 T3 RC1 RC2 RC3 
S1 L1 1 1.5 NULL 45 R F T
S1 L1 2 2.5 2 NULL 35 F G
S1 L2 1 4 3 NULL F T R
S2 L1 1 56 45 24 F G Y
S2 L2 1 10 5 NULL G F Y
S2 L2 2 20 NULL 34 F G T
S3 L1 1 3.4 NULL 32 F T Y
S3 L2 1 4.6 3 21 D D R

T1
T2
T3
T4

   S2 S1 S3
G1 11 12 13
G2 21 22 23
G3 31 32 33
G4 41 42 43

     
   S2 S1 S3
T1_L1 56 2 3.4	  
T1_L2 15 4 4.6
T2_L1 45 2 NULL 
T2_L2  5 3 3
T3_L1 24 45 32
T3_L2 34 NULL 21

awk ' FILENAME=="QUERY.TXT" { cols[$0];next }
      FILENAME=="data.txt"  && NR==1 {
        for(i=1; i<=NF; i++)
        {
        if ($i=="Sample")
        s[1]=i
        if ($i=="Loc")
        s[2]=i
        if ($i=="Rep")
        s[3]=i
        }
        next;
  }
  {
    
    for(i=1; i<=NF; i++)
      if(($i in cols))
       for(j=1; j<=p; j++) {
               st=a[j]
               for(i in s){
                   st=st" "s[j];
               }
        print st }
    if  !($i in cols)
        delete s["i"];
    }
'  QUERY.TXT data.txt data.txt mat.txt