Table 1

Summary of read alignments
Naive reference Cured reference
Sample Experiment Type No. sequence reads No. sequence reads mapped to reference

Aligned reference sequence

/bases

Average depth over aligned reference No. unigenes with mapped sequence reads Total sequence mapped to naive reference/Gb No. sequence reads mapped to A genome No. A genome unigenes with mapped sequence reads No. sequence reads mapped to C genome No. C genome unigenes with mapped sequence reads

Aligned reference sequence

/bases

Average depth over aligned reference Total sequence mapped to cured reference/ Gb

Increase sequence mapped to reference

/ %

B. napus 1 rep1 BCC_1_2* Resynthesized (B. rapa cytoplasm) 30290727 11396746 27704492 32.9 60801 0.91 8136121 57101 7725545 57232 48716080 26.0 1.27 39.2
B. napus 1 rep2 BCC_2_2_rep* 32362747 12596459 27628537 36.4 60182 1.01 8974130 56758 8472600 56859 48927782 28.5 1.40 38.5
B. napus 1 rep3 BCC_3_2* 30212318 12688970 28367947 35.8 60953 1.02 8933134 57381 8523534 57505 50115239 27.9 1.40 37.6
B. napus 1 rep4 BCC_4_2* 29073842 12556527 27816387 36.1 60572 1.00 8886730 57072 8581997 57168 49020495 28.5 1.40 39.1
B. napus 2 rep1 BCC_1_4* Resynthesized (B. oleracea cytoplasm) 28333122 11390102 28050282 32.5 61139 0.91 8138583 57406 7545728 57600 49388101 25.4 1.25 37.7
B. napus 2 rep2 BCC_2_4* 27156815 11209306 27415043 32.7 59994 0.90 7908682 56465 7619986 56551 48167524 25.8 1.24 38.5
B. napus 2 rep3 BCC_3_4* 29720775 12618159 28214425 35.8 61051 1.01 8828851 57410 8491265 57632 49691719 27.9 1.39 37.3
B. napus 2 rep4 BCC_4_4* 29830870 12580532 28294428 35.6 61303 1.01 8829979 57645 8473127 57779 49861276 27.8 1.38 37.5
Tapidor TAP** Winter 22841910 11026783 28473370 31.0 61776 0.88 6770387 57940 7281348 58231 48844912 23.0 1.12 27.4
Ningyou 7 NIN** Chinese 23151184 10774087 28233727 30.5 61982 0.86 6640976 58055 6841509 58167 48266879 22.3 1.08 25.1
Altasweet D3_ALT* Swede 29080184 13239756 28730927 36.9 61251 1.06 8340513 58022 8806044 58177 49777567 27.6 1.37 29.5
Ceska D31_CES* Spring 28036702 13193597 29567877 35.7 61903 1.06 8050594 58512 8803320 58830 51209098 26.3 1.35 27.7
Aphid Resistant Rape D8_AphRR* Fodder 28334337 11879400 29161922 32.6 62434 0.95 7486610 58922 7881247 59083 50269176 24.5 1.23 29.4

* deposited under SRA accession ERA063602.

**deposited under SRA accession ERA036824.

Higgins et al.

Higgins et al. BMC Genomics 2012 13:247   doi:10.1186/1471-2164-13-247

Open Data