Figure 2. Deﬁnition of gene hits at GABI-Kat. (a) For protein-coding genes with annotated UTR-regions in TAIRv10, we differentiate between CDSi hits (insertion position between ATG and STOP), 50- and 30-TS2TE hits (insertion position in the 50- or 30-UTR) and promoter hit [insertion position up to 300-bp upstream of transcription start (TS)]. (b) If the UTR is not annotated in TAIRv10 (and for pseudogenes), insertion positions 300-bp up or downstream of ATG and STOP are considered as 50- and 30-hits. (c) For RNA genes and transposable elements, TS2TE hits are annotated, if the insertion is located between TS and transcript end. introns). We extended this deﬁnition by including hits in the transcribed region of a gene as well as the promoter region (Figure 2). ‘TS2TE hits’ have an insertion between transcription start and transcript end, and ‘promoter hits’ have the predicted insertion position within 300-bp upstream of the transcription start. This deﬁnition applies for protein- as well as for RNA-coding genes. If no UTR is annotated for a given gene, we still use the old gene hit deﬁnition. All hits that are not linked to a gene keep the insertion type ‘genome hit’ (Figure 2). Due to the fact that the old ‘gene hit’ deﬁnition covered a larger genome area than the TS2TE area of the genome, the total number of insertions that qualify as ‘gene hits’ went slightly down, although the number of predicted in- sertions in the database did increase. The updated inser- tion types allow a more reliable selection of insertion alleles that may be alleles. Overall, the total number of lines with predicted inser- tions was increased to 71 235. Table 1 gives a summary of the current data content of the SimpleSearch database. Increase of quality and accuracy of the database content Due to the manual handling steps during the generation of the GABI-Kat population, it is an unpleasant fact that some links between FST sequences and insertion lines are wrong. Reasons for these errors can be mix-ups during plant growth in the greenhouse, handling errors during sequence generation, or alike. Incorrectly assigned FST-sequences were detected when the conﬁrm- ation rate in a set of 96 lines (corresponding to a microtitre plate) was much lower than expected from average values. Based on the knowledge about the FST production workﬂow, we deduced different types of errors that might have happened and reassigned the FST-sequences to the correct lines after wet-lab validation of the hypoth- esis. This reassignment of FST-sequences has meanwhile been performed for the majority of problematic microtitre Nucleic Acids Research, 2012, Vol. 40, Database issue D1213 Table 1. Summary of data in the GABI-Kat SimpleSearch databasea Data type FSTsb Linesb with segregation data available at NASC Insertions with predicted insertion positionc analysed with ﬁnal resultd delivered to individual users conﬁrmed and available at NASCe Distinct genes covered protein coding genes ncRNA coding genes pseudogenes transposable element genes Gene hits available only from GABI-Katf Conﬁrmed ‘GABI-Kat only’ hits at NASC ‘GABI-Kat only’ hits to be adressedg Distinct CDSi covered Number of entries 133 000 71 235 15 289 9644 88 580 16 081 6816 9653 21 005 19 120 182 420 1283 2114 1201 765 13 037 aNumbers as of 15 September 2011. bDatabase release version 24 (affects FSTs and lines that are in the database, the data values for the items in the database are updated every 24 h). cInsertions are different from lines, because a line can contain several insertions. Example: 011F01, which is conﬁrmed for a genome hit at F26P21 (Chr4) and a TS2TE hit in At5g05180. dA ﬁnal result can be ‘conﬁrmed’, but also ‘failed to conﬁrm’ or ‘part of a contamination group’ are considered. eFor each conﬁrmed insertion there are conﬁrmation sequences avail- able which are generated from the amplicon that spans the T-DNA/ genome sequence junction. fOnly hits that may cause a allele (CDSi hits and hits in the 50-UTR) are counted. Only lines in the accession Columbia-0 are con- sidered, which is the accession used by the main FST-based insertion line collections. gAbout 150 ‘GABI-Kat only’ alleles are either in the queue already and wait for mature T3 seed, or did fail to conﬁrm. plates and contributed to a signiﬁcant increase ( 3%) of the conﬁrmation rate of insertion alleles from the collection. The corrected FST-to-line connections have been integrated into the database and are available to users through SimpleSearch. It should be noted that SimpleSearch is currently the only source of these correc- tions. Until other FST databases have been updated, the now detected and corrected errors in the original FST dataset are still ‘proliferated’ from e.g. the old FST data in sequence databases. When predictions for very similar insertion sites are found in multiple lines, we combine these lines into ‘con- tamination groups’. The assumption is that the prediction is only true for one of those lines and the others are caused by contaminations that happened during high-throughput DNA-preparation, PCR, or sequencing. If an insertion that is part of a contamination group is ordered by a user, the whole contamination group is examined experi- mentally. Finally, the correct insertion is delivered to the user and donated to the Nottingham Arabidopsis Stock Centre (NASC). In some cases, several alleles are con- ﬁrmed with closely linked insertion positions, and in these cases all alleles except one conﬁrmed allele are removed from the ‘contamination group’. SimpleSearch contains information about failed insertion conﬁrmations