Genome-wide characterization of non-reference transposons in crops suggests non-random insertion

BMC Genomics

Table 1 Summary of the non-ref TEs in rice, maize, sorghum

Species	Groups	Sample size	Total reads	Raw data depth	Average depth	Non-ref TEs	Average non-ref TEs	NPSPD^a	Average length^b	% in genome^c
O. stativa		50	3901075202	934.61	18.69	13066	261	0.28	24312832	0.064
	Improved	11	929384266	213.98	19.45	2744	249	1.17	5238995	0.014
	Landrace	29	2173501326	533.99	18.41	8914	307	0.58	16703160	0.044
	Wild	10	798189610	186.64	18.66	5175	518	2.77	9477388	0.025
Z. mays		30	3717985422	182.96	6.10	23866	796	4.35	41408468	0.020
	Improved	6	1079477218	52.24	8.71	9846	1641	31.41	17762074	0.009
	Landrace	23	2530119502	124.94	5.43	15628	679	5.44	26251683	0.013
	Wild	1	108388702	5.78	5.78	1798	1798	311.07	3150689	0.002
S. bicolor		45	7633325734	891.37	19.81	35679	793	0.89	53089501	0.072
	Improved	20	3574432140	397.59	19.88	19980	999	2.51	29721648	0.040
	Landrace	18	2678808170	325.89	18.10	15437	858	2.63	22776676	0.031
	Wild	7	1380085424	167.89	23.98	17941	2563	15.27	25363817	0.034

ISSN: 1471-2164