Table 1 |
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|
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). |
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|
Schwartz et al. BMC Genomics 2010 11:694 doi:10.1186/1471-2164-11-694 |
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