Assessment of genetic variation for the LINE-1 retrotransposon from next generation sequence data

BMC Bioinformatics

Table 1 Description of the LINE-1 insertion sites identified in this study

Chromosome	Insert Site Position	NA12878 genotype	NA12891 genotype	NA12892 genotype	LINE-1 Orientation	Gene Locus	Entrez ID	Gene orientation
Chr_2	144021434	+/-	+/-	N	-	ARHGAP15	55843	+
Chr_3	38601086	+/-	+/-	+/-	+	SCN5A	6331	-
Chr_3	82073683	+/-	Y	N	-
Chr_3	125073416	Y	+/-	Y	+	MYLK	4638	-
Chr_3	187854832	+/-	N	Y	+
Chr_4	132401098	+/-	+/-	+/-	-
Chr_4	147444745	+/-	N	Y	+	SLC10A7	84068	-
Chr_5 (*)	21243489	Y	+/-	+/-	+
Chr_5	89486537	Y	Y	Y	+
Chr_6	102952779	+/-	+/-	N	-
Chr_6 (*)	123895635	+/-	+/-	N	-	TRDN	10345	-
Chr_7 (*)	7985552	+/-	N	+/-	+	GLCCI1	113263	+
Chr_7	53619996	+/-	Y	?/?	-
Chr_10	124445220	Y	+/-	Y	+
Chr_11	109883089	Y	N	+/-	-
Chr_12	125368882	+/-	N	+/-	-
Chr_13	60360333	Y	Y	+/-	-
Chr_14	51737509	Y	Y	Y	-
Chr_15	31819131	Y	+/-	+/-	-	RYR3	6263	+
Chr_15	54038444	+/-	N	+/-	+	NEDD4	4734	-
Chr_17 (*)	62067756	+/-	+/-	N	+	PRKCA	5578	+
Chr_18	12481262	+/-	N	+/-	+	SPIRE1	56907	-

Legend: Position and genotype for the twenty two LINE-1 putative full length insertions identified in this work. The splice site position is the position of the base nearest the 5′ most base of the LINE-1 insertion in the human genome assembly build 36.3. A ‘Y’ genotype indicates that all reads found for that individual at that position contained the LINE-1 insert. An ‘N’ genotype indicates that no reads found for that individual at that position contained the LINE-1 insert. A ‘+/-‘ genotype indicates the individual was heterozygous at that position, and ‘?/?’ indicates that no reads could be found for that individual at that position. The L1 orientation of + and – indicate sense and antisense insertion respectively with respect to the assembly. Those rows marked with an (*) were verified by PCR.

ISSN: 1471-2105