A T-DNA mutant screen that combines high-throughput phenotyping with the efficient identification of mutated genes by targeted genome sequencing

Table 1 Filtering of sequencing reads improves mapping to the Arabidopsis genome

	Library I		Library II
	No. of reads	%	No. of reads	%
Total sequencing reads	207,785	100.0	154,847	100.0
1. Filter: T-DNA containing reads	163,166	78.5	116,160	75.0
2. Filter^a: HSP length, e-value	1536	0.7	3932	2.5
3. Filter^b: Read length and quality, removal of adapter-only and vector-only reads	264	0.1	374	0.2
Mapped to the Arabidopsis genome	255	0.1	367	0.2

^a BLASTN search against the pBIN-PROK2 sequence with the settings: High-scoring segment pair (HSP) length ≥ 30 bp to ≤343 bp, E value ≤5.72*E⁻¹¹; ^b read length > 40 bp, low quality limit 0.05, ambiguous bases ≤2, removal of the 5′ terminal nucleotide, removal of adapter-only and vector-only sequences

ISSN: 1471-2229