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In silico validation of programs on the Pyrus communis genome by BLAST searches against the National Center for Biotechnology Information RefSeq mRNA database.

 
Program Validated Uncertain Unaligned Rearranged Chimeric
Rascaf 1218 42 13 4 9
L_RNA_scaffolder 474 128 24 38 43



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Evaluation of Arabidopsis thaliana assemblies for single RNA sequencing (RNA-seq) data (top) and with 0, 1, …, 11 RNA-seq data sets (bottom), using Quast (Gurevich et al., 2013).

 
Programs Raw assembly Rascaf Rascaf+BWA-mem L_RNA_ scaffolder AGOUTI
Single RNA-seq set (SRR2187604)
 Scaffolds 8082 7686 7674 7759 7771
 NGA50† 42,479 46,331 46,828 44,441 45,667
 Misassemblies 1153 1180 1188 1296 1177
 Problematic scaffolds 1412 1434 1434 1536 1433
 Effective misassemblies na 10 14 114 10
Multiple RNA-seq sets
 Data sets 0 (raw) 1 2 6 11
 Scaffolds 8082 7686 7626 7283 7222
 NGA50 42,479 46,331 46,898 49,673 50,571
 Misassemblies 1153 1180 1190 1281 1302
 Problematic scaffolds 1412 1434 1437 1473 1478
 Effective misassemblies na 10 14 66 77
NGA50 is defined as the minimum length of a scaffold alignment such that 50% of the aligned portion of the assembly to the reference genome is in scaffold alignments this size or longer.



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Summary of quality indicators for the original (raw) assemblies of the sequenced Fragaria species (Hirakawa et al. 2014).

 
Assembly No. of scaffolds Total length N50†
bp
F. iinumae (v1.0) 117,822 199,627,645 3309
F. nipponica (v1.0) 215,024 206,414,979 1275
F. nubicola (v1.0) 210,780 203,686,576 1291
F. orientalis (v1.0) 323,163 214,184,046 722
F. × ananassa (v1.0) 625,966 697,765,214 2201
N50 is the minimum length of a scaffold such that half of the assembled genome sequence is in scaffolds of this size or longer.



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In silico evaluation of predicted Rascaf connections in the Fragaria genomes by BLAST searches against the NCBI RefSeq mRNA database.

 
Species Validated Uncertain Unaligned Rearranged Chimeric
Rascaf with ERR430941 (F. × ananassa)
F. iinumae 5267 119 19 16 28
F. nipponica 7496 155 32 20 35
F. nubicola 8447 198 59 26 59
F. orientalis 10,147 279 112 16 72
F. × ananassa 5866 365 201 44 109
Rascaf with SRR1930097 (F. vesca)
F. iinumae 1613 5 0 1 0
F. nipponica 2710 6 1 1 3
F. nubicola 3644 14 5 6 3
F. orientalis 3880 25 9 2 7
F. × ananassa 1876 36 9 6 8



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Evaluation of gene content for the five Fragaria assemblies before and after improvement using RNA sequencing (RNA-seq) data. Shown are the numbers of transcripts with 90% or more base coverage as well as the total number of transcripts that experienced gains in coverage.

 
Data set Transcripts with >90% coverage
Gain (>0) Gain (>5%)
Before After
RNA-seq accession: ERR430941
F. iinumae 10,800 14,562 6931 6684
F. nipponica 5997 8918 9399 8967
F. nubicola 6468 9772 9928 9470
F. orientalis 1747 3262 11,033 10,302
F. × ananassa 6325 6711 3812 3192
RNA-seq accession: SRR1930097
F. iinumae 10,800 11,699 1899 1816
F. nipponica 5997 6722 2782 2543
F. nubicola 6468 7495 3703 3441
F. orientalis 1747 2222 3687 3263
F. × ananassa 6325 6445 1019 834