Supplementary Table S4 Comparison of QIIME and Pyrotagger Outputs of 454 Sequencing

Supplementary Table S4 Comparison of QIIME and Pyrotagger outputs of 454 sequencing

Sample / Number of Reads / Number of OTUsa / Diversity indices (Shannon/Simpson)
QIIME / Pyrotagger / QIIME / Pyrotagger / QIIME / Pyrotagger
D. ananassae / 30005 / 23916 / 42 / 20 / 1.96/0.75 / 0.38/0.17
D. deflecta / 61398 / 50547 / 318 / 430 / 3.43/0.88 / 3.13/0.85
D. duncani / 36048 / 29827 / 108 / 98 / 1.67/0.58 / 0.93/0.36
D. erecta / 27813 / 21953 / 44 / 17 / 1.63/0.69 / 0.60/0.37
D. falleni / 39194 / 30726 / 223 / 241 / 2.89/0.89 / 2.82/0.88
D. melanogaster1 / 34969 / 29373 / 41 / 16 / 1.22/0.51 / 0.62/0.33
D. melanogaster2 / 47495 / 41874 / 48 / 24 / 1.14/0.47 / 0.66/0.34
D. melanogaster AZ / 10776 / 8991 / 178 / 145 / 2.60/0.82 / 2.19/0.78
D. melanogaster NY1 / 35405 / 30939 / 61 / 39 / 1.80/0.65 / 1.60/0.61
D. melanogaster NY2 / 29108 / 18331 / 110 / 82 / 2.27/0.79 / 2.08/0.81
D. munda / 28902 / 22167 / 195 / 223 / 3.04/0.88 / 2.73/0.85
D. neotestacea / 32058 / 27529 / 71 / 116 / 2.09/0.80 / 1.97/0.78
D. persimilis / 26811 / 22425 / 35 / 5 / 0.71/0.31 / 0.08/0.02
D. pseudoobscura / 30005 / 24048 / 130 / 68 / 1.98/0.78 / 0.84/0.52
D. quinaria1 / 41359 / 32111 / 204 / 216 / 3.05/0.91 / 2.27/0.82
D. quinaria2 / 53052 / 43338 / 224 / 267 / 3.04/0.91 / 2.32/0.82
D. santomea / 33747 / 28400 / 46 / 21 / 1.59/0.69 / 1.05/0.58
D. sechellia / 36645 / 29959 / 62 / 30 / 2.14/0.82 / 1.3/0.67
D. simulans / 51702 / 43181 / 36 / 12 / 1.27/0.55 / 0.16/0.06
D. suboccidentalis / 42494 / 35516 / 194 / 180 / 2.01/0.70 / 1.68/0.64
D. virilis / 43862 / 39451 / 64 / 45 / 0.88/0.35 / 0.50/0.2
D. willistoni / 40727 / 34389 / 48 / 26 / 1.75/0.73 / 0.84/0.52
D. yakuba / 45603 / 38138 / 62 / 18 / 1.63/0.71 / 0.75/0.50

a The operational taxonomic units (OTUs) were defined with pair-wise 97% sequence identity