Deep landscape update of dispersed and tandem repeats in the genome model of the red jungle fowl, Gallus gallus, using a series of de novo investigating tools

Table 4 Features and diversity of TE models found in the galGal4 model based on the REPET and DM annotations (STEP3 + STEP4, Fig. 2) after stack resolving and merging stacked and juxtaposed annotations

Names of TE models	a	b	c^a	d	e
CR1	308	LINE	413857	66.4707	11.8457
Ancestral_LTR_group_1	3	LTR	86	0.0138	0.0034
Ancestral_LTR_group_2	1	LTR	22	0.0035	0.0013
Ancestral_LTR_group_3	1	LTR	40	0.0064	0.0012
Ancestral_LTR_group_4	1	LTR	308	0.0495	0.0119
BIRDDAWG	10	LTR	6238	1.0019	0.2525
EAV	1	LTR	191	0.0307	0.0212
EAV-HP	7	LTR	765	0.1229	0.0496
ERV2	2	LTR	426	0.0684	0.0209
ERV7	10	LTR	2885	0.4634	0.1061
ERV11	1	LTR	512	0.0822	0.0168
Kronos	46	LTR	30732	4.9359	0.7377
putative_LTR_group4	2	LTR	835	0.1341	0.0137
putative_LTR_group9	1	LTR	170	0.0273	0.0017
putative_LTR_group12	17	LTR	1797	0.2886	0.05
putative_LTR_group22	3	LTR	1219	0.1958	0.0257
putative_LTR_group28	2	LTR	367	0.0589	0.0116
putative_LTR_group30	13	LTR	3847	0.6179	0.0996
retroCalimero	1	LTR	826	0.1327	0.0540
retroSaturnin	1	LTR	161	0.0259	0.0118
retroTux	2	LTR	2490	0.3999	0.1243
Soprano	19	LTR	3014	0.4841	0.1171
Charlie	3	TIR	37319	5.9939	0.5868
Charlie-Galluhop	5	TIR	67691	10.872	1.0296
Galluhop	2	TIR	4588	0.7369	0.1198
Mariner1_GG	10	TIR	5686	0.9132	0.1491
Hitchcock	4	undefined	27033	4.3418	0.4182
undetermined_group_1	3	undefined	2219	0.3564	0.0773
undetermined_group_2	2	undefined	1030	0.1654	0.0165
undetermined_group_3	2	undefined	174	0.0279	0.0045
undetermined_group_4	4	undefined	2550	0.4096	0.0423
undetermined_group_5	2	undefined	134	0.0215	0.0036
undetermined_group_6	1	undefined	372	0.0597	0.0100
Z_rep	9	undefined	3032	0.487	0.1476
Total	499		622616	100	16.1832^b

a, Number of consensus; b, TE types; c, Total number of TE copies; d, Percentage of the total number of TE copies; e, Percentage of chromosome coverage; ^aPost stack resolving and annotation merging are called copies all complete elements, internally deleted elements; 5' or 3' truncated elements and elements truncated at both ends (i.e. internal regions of a TE devoid of ends). ^bthis coverage value was more elevated than the 15.7 % indicated in the main text because the coverage corresponding to the small TE copies nested in larger TEs were not removed for these calculations

ISSN: 1471-2164