Table 9: Summary statistics for the mapping of several read datasets against the cork oak draft genome.

From: The draft genome sequence of cork oak

Study and data type SRA accession number Total number of reads Number of mapped reads Percentage of mapped reads
Magalhães et al.3 (454)        
 Medium drought SRR1812375 587,184 439,362 74.8
 Severe drought SRR1812376 473,117 342,671 72.4
 Well-watered SRR1812377 645,761 484,889 75.1
Rocheta et al.4 (454)        
 Male flower SRR1609152 659,399 493,298 74.8
 Female flower SRR1609153 535,665 401,025 74.9
Teixeira et al.39 (454)        
 Good cork quality SRR1009171 573,548 409,169 71.3
 Bad cork quality SRR1009172 600,102 417,493 69.6
Sebastiana et al.2 (454)        
 ECM roots SRR1012033 1,159,845 769,423 66.3
 Non-symbiotic roots SRR1012034 969,271 636,048 65.6
Somatic embryogenesis (Illumina PE)        
 Embryo globular stage SRX2239661 71,706,998 62,998,568 87.9
 Embryo heart/torpedo stage SRX2239662 71,964,732 64,487,926 89.6
 Embryo immature cotyledonary stage SRX2239663 84,482,546 73,969,188 87.6
 Embryo mature cotyledonary stage SRX2239664 84,022,498 73,715,150 87.7
Chaves et al.40 (Illumina SE)        
 Leaf SRR988108 16,838,439 13,900,006 82.5
 Cork SRR988109 9,333,712 7,223,415 77.4
HL8 RNA-Seq (Illumina PE)        
 Pollen SRR5986741 192,418,402 161,872,000 84.1
 Leaf SRR5986739 299,960,018 245,400,286 81.8
 Xylem SRR5986738 361,255,569 296,903,800 82.2
 Inner bark SRR5986740 311,378,053 251,537,756 80.8
 Phellem SRR5986737 353,687,405 285,006,172 80.6
  1. The reads were downloaded from NCBI’s Sequence Read Archive and mapped to the draft genome using BWA-mem.