supplementary figure 1 . regional assembly supplementary table 1 . bacterial data sets used to test polymorphism discovery with vaal supplementary table 2 . nature of called , uncalled polymorphisms of m. tuberculosis f11 vs h37rv supplementary table 3 . effect of depth of sequence coverage on discovery of polymorphisms in m. tuberculosis f11 vs h37rv supplementary table 4 . effect of depth of sequence coverage on discovery of polymorphisms in m. tuberculosis f11 vs h37rv , using vaal and velvet + vaal steps 3,4 supplementary table 8 . vibrio cholerae : observed differences between resistant isolates and their sensitive parents , found using velvet ( + vaal steps 3,4 ) supplementary methods supplementary results supplementary references supplementary resources