Table 1

Reference mapping results of type strain Alcanivorax borkumensis SK2 using pyrosequencing reads and comparison with de novo assembly (MIRA3)
SOFTWARE Total bps covered by mapping/Length of missing fragments Disagreements Number of bps
MOSAIK 3 099 937
20 206
Ns 1535
Tranversion/Transitions 2
Insertions 10 225
Deletions 7 733
NEWBLER 3 104 799
15 344
Ns 1 544
Tranversion/Transitions 0
Insertions 11 493
Deletion 10 346
MIRA3 3 119 125
1 018
Ns 905
Tranversion/Transitions 2
Insertions 1 867
Deletions 5 187
de novo 3 079 251
40 892
Ns 323
Tranversion/Transitions 9 814
Insertions 1 491
Deletions 1 590

The difference between NC_008260 (3,120,143 bps) and the number of nucleotides covered corresponds to the total length of the genome not mapped. Disagreements are indicated as conflicting positions in the consensus sequence between reference genome and mapped reads. Ns – number of fully ambiguous nucleotides within mapped regions.

Kisand and Lettieri

Kisand and Lettieri BMC Genomics 2013 14:211   doi:10.1186/1471-2164-14-211

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