Table 2.

Annotations of insertion sites that were not confirmed with PCR assays

Blast Cluster/Read Name	MAGI4.0 hit	Insertion site	ZMGI hit	Insertion type	Annotation/Expression Pattern	Likely cause for failure to amplify
03S-0467-13A2-G01	repeat hit only		DR906457	exon	egg cell expressed	primer design error
bc0041	MAGI4_104	252	no hit		No EST support for gene	primer design error
bc0093	MAGI4_65387	128	DN229926	exon	leaf & SAM expressed	unknown
bc0182	MAGI4_121677	no MuTIR	no hit		No EST support for gene	primer design error
bc1042	MAGI4_128194	1502	no hit		No EST support for gene	primer design error
bc1073	MAGI4_94877	3164	TC303220	exon	TM20/Dek34 gene	low quality sequence
bc1382	repeat hit only	no MuTIR	no hit		Novel maize genomic sequence	low quality sequence
bc1435	MAGI4_132661	no MuTIR	DT943333	unknown	thioesterase superfamily	low quality sequence
bc1509	repeat hit only		no hit		Novel maize genomic sequence	primer design error
bc1526	MAGI4_13062	no MuTIR	TC292893	unknown	26S protease regulatory subunit 7	unknown
bc1537	MAGI4_5849	481	TC291433	intron	cold stressed seedling expression	low quality sequence
bc1571	MAGI4_154704	734	TC282381	-40bp	short-chain dehydrogenase/reductase	unknown