Table 1

Summary of A. hypochondriacus 454 sequencing data trimming, assembly and annotation

Run Metrics

Total raw reads

2,913,966 (100%)

Total bases

909,631,600

Reads after quality control and trimming

2,700,168 (92.6%)

Bases entering assembly

877,153,000 (96.4%)


Assembly

Aligned reads

2,417,008 (89.5%)

Aligned bases

803,229,499 (88.3%)

Assembled reads

1,886,081

Fully assembled

1,422,449

Partially assembled

463,632

Singletons (5.9)

178,636

Repeats

68,980

Outliers

56,216

Too short

46,623


Isogroup Metrics

Total isogroups

15,667

Average contig content

3.0

Largest contig content

22,172

Number with one contig

12,739

Average isotig content

1.3

Largest isotig content

52

Number with one isotig

12,950


Isotig metrics

Total isotigs

20,408

Average contig content

1.7

Largest contig content

17

Number with one contig

12,985

Number of bases

20,710, 069

Average isotig size

1, 014

N50 isotig size

1,196

Largest isotig size

4,762


Large contig metrics

Number of contigs

15,608

Number of bases

15,170,717

Average contig size

971

N50 contig size

1,063

Largest contig size

3,379


All contig metrics

Number of contigs

25,998

Number of bases

18,043,010


Annotation (contigs/isotigs)

nr (NCBI)

17,282

TAIR

16,597


Annotation (singletons)

UniRef 100

17,440

UniRef 50

4,396

Amaranthaceae ESTs

10,846

TAIR

≈1,000


Délano-Frier et al. BMC Genomics 2011 12:363   doi:10.1186/1471-2164-12-363

Open Data