Negative start position bed file

[chariko]

I aligned two samples (bwa; filter with samtools, removed duplicates with picard-tools, bamtobed and bed to bedgraph with genomeCoverageBed) to a genome file consisting in 4 genes and the first sample went fine but the second one when getting the bed file the start position for one of the genes was -1. I wonder that is not correct but I do not know why did I obtain such negative value.

Example:

"Wrong bed file for gene1"
gene1 -1 150 M00... 37 -
gene1 -1 150 M01... 37 +
gene2 1004 1115 M00... 60 -

I realized that -1 values in special cases, however, BEDPE (bed paired end) positions may be set to -1 to indicate that one or more ends of a BEDPE feature is unaligned.

http://bedtools.readthedocs.org/en/latest/content/overview.html

but I do not understand if that´s my case and I really do not understand why did it align if it was unaligned....

Any clues?