I am using the command

bedtools multicov [OPTIONS] -bams BAM1 BAM2 BAM3 ... BAMn -bed <bed gff="" vcf="">

for the bedtools to get the count matrix and the output I get is like this :

chr4    251355  266500  CG1674-RB   0   +   252579  266389  0   11  166,43,570,81,81,81,291,85,320,115,695, 0,1205,1549,3535,4134,5665,6539,9584,12536,12904,14450, 801
chr4    252055  266500  CG1674-RC   0   +   252579  266389  0   9   198,43,81,81,291,85,320,115,695,    0,505,2835,4965,5839,8884,11836,12204,13750,    785
chr4    252108  265205  CG1674-RA   0   +   252579  264217  0   12  122,43,570,81,81,291,117,85,138,219,483,162,    0,452,796,2782,4912,5786,7639,8831,9213,10978,11783,12935,  600
chr4    380577  395610  CG1710-RC   0   +   381316  393018  0   13  24,420,310,212,189,146,1074,1089,238,155,267,364,2735,  0,635,2352,2719,2994,3542,3916,5722,9555,9858,11139,11861,12298,    1625
chr4    380587  395610  CG1710-RB   0   +   381316  393018  0   13  19,420,310,212,189,146,1074,1089,238,155,267,364,2735,  0,625,2342,2709,2984,3532,3906,5712,9545,9848,11129,11851,12288,    1625
chr4    380602  395610  CG1710-RD   0   +   381316  393018  0   13  43,420,310,212,189,146,1074,1089,238,155,267,364,2735,  0,610,2327,2694,2969,3517,3891,5697,9530,9833,11114,11836,12273,    1625
chr4    380602  395610  CG1710-RA   0   +   381316  393018  0   13  308,420,310,212,189,146,1074,1089,238,155,267,364,2735, 0,610,2327,2694,2969,3517,3891,5697,9530,9833,11114,11836,12273,    1625
chr4    650318  655978  CG1732-RA   0   +   650461  655137  0   10  287,268,102,181,268,104,370,204,168,943,    0,1934,2335,2515,2755,3636,3798,4228,4484,4717, 4
chr4    650318  655978  CG1732-RB   0   +   650461  654676  0   10  287,268,102,181,268,104,370,164,168,943,    0,1934,2335,2515,2755,3636,3798,4268,4484,4717, 4
chr4    745029  796720  CG32019-RC  0   +   746342  796175  0   41  88,361,22,163,142,224,403,674,348,45,123,60,99,309,126,39,228,174,36,148,374,126,700,354,1713,900,764,136,891,2673,282,300,9471,979,342,1043,57,101,127,303,1180,   0,1265,2258,3057,3700,6373,6659,7156,8813,9516,9875,10074,10310,11111,11501,11745,12415,13332,14549,17999,18384,20762,20968,22072,22903,26166,27773,28621,28934,29883,33117,33461,33816,43358,44400,46149,47999,49613,49781,49973,50511,    2
chr4    745029  796720  CG32019-RD  0   +   746342  796175  0   46  88,361,22,163,142,133,201,302,224,403,674,348,45,123,60,99,309,126,39,177,228,174,36,33,148,374,126,700,354,1713,900,764,136,891,2673,282,300,9471,979,342,1043,57,101,127,303,1180,    0,1265,2258,3057,3700,4278,4598,4870,6373,6659,7156,8813,9516,9875,10074,10310,11111,11501,11745,11935,12415,13332,14549,15545,17999,18384,20762,20968,22072,22903,26166,27773,28621,28934,29883,33117,33461,33816,43358,44400,46149,47999,49613,49781,49973,50511, 2

I am using it for one bam file at a time and the bed file was downloaded from ucsc. I was expecting something like the count matrix generated by ht-seq. Is this output correct? (I am using default options)