Table 1

Summary statistics for 454 sequencing and de novo assembly.

Female

Male

Total


Total number of raw reads

538,706

753,163

1,291,869


Number of reads after cleaning

507,466

730,814

1,238,280


Amount of cleaned data

207 Mbp

246 Mbp

453 Mbp


Average length of cleaned reads (bp)

408

337

366


NEWBLER contigs (large > 500 bp)

NA

NA

82,134 (30,520)


NEWBLER contig bp total

NA

NA

48 Mbp


NEWBLER contig length (bp)

NA

NA

90-10,680 (avg 581)


Average coverage (NEWBLER)

NA

NA

7.6×


Reads placed (NEWBLER)

NA

NA

1,035,854


Singletons (after NEWBLER)

NA

NA

134,971


MIRA contigs

NA

NA

14,245


Reads placed (MIRA)

NA

NA

33,093


Singletons mapped by BLAST to contigs

NA

NA

5846


Reads discarded1

NA

NA

70,926 (5.7%)


Remaining Singletons

NA

NA

92,561 (7.5%)


Total reads placed

NA

AN

1,074,793 (86.8%)


Total number of contigs

NA

NA

96,379


SNPs

NA

NA

95,295


INDELs

NA

NA

31,651


454 GS-FLX Titanium chemistries were used to sequence normalized sex-specific pools of cDNA.

1Reads were discarded either due to redundancy (3461) or for quality control by NEWBLER or MIRA during the assembly process (67,455 and 10 respectively).

Schwartz et al. BMC Genomics 2010 11:694   doi:10.1186/1471-2164-11-694

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