Table 9

GAGE statistics (SNPs, indels and misjoins) on human chromosome 14.

Assembler

SNPs

Indels < 5 bp

Indels ≥ 5 bp

Misjoins

Inv

Reloc


Allpaths-LG

55319

27563

2558

101

44

57

CABOG

81151

28438

2884

149

46

103


Allpaths-LG + CABOG

GAM-NGS

61725

29936

2950

119

32

87

GAA

63835

30151

2990

123

29

94


CABOG + Allpaths

GAM-NGS

79478

29653

3021

154

43

111

GAA

81763

29812

3008

134

31

103


For each assembly we show the number of SNPs, the number of indels shorter than 5 bp and greater (or equal) than 5 bp. The number of misjoins is computed as the sum of inversions (parts of contigs reversed with respect to the reference genome) and relocations (rearrangements moving a contig within/between chromosomes). All the statistics were computed using the same script with the gapped reference genome (107,349,540 bp).

Vicedomini et al. BMC Bioinformatics 2013 14(Suppl 7):S6   doi:10.1186/1471-2105-14-S7-S6

Open Data