mapper graph doesn't match # reads

[InaMBerry]

Noticed a discrepancy for some samples. Sample 14045 actually has >500K reads (see flagstats file) but in the figure it shows as only unmapped reads (<100K). I do not know why the figure doesn't show the reads that mapped. I would have sent this sample for re-sequencing based on the figure but Kat noticed that it mapped when ran with a single reference. We need to figure out why this is and fix it so we don't re-sequence unnecessarily.
flagstats.txt

[averagehat]

Are any of the other samples showing only unmapped reads wrong? Like 14084 or 14059 are showing only unmapped reads also.