Genetic diversity and population structure of trifoliate yam (Dioscorea dumetorum Kunth) in Cameroon revealed by genotyping-by-sequencing (GBS)

Siadjeu, Christian; Mayland-Quellhorst, Eike; Albach, Dirk C.

doi:10.1186/s12870-018-1593-x

Table 2 Summary statistics of filtering and clustering GBS data from D. dumetorum

From: Genetic diversity and population structure of trifoliate yam (Dioscorea dumetorum Kunth) in Cameroon revealed by genotyping-by-sequencing (GBS)

Accessions code	Raw reads	clusters total at 85%	Heterozygosity (ɛ)	Sequence error rate (Π)	Consensus reads	Loci with 75% of samples	Mean depth
A07W	97,6092	85,513	0.01	0.006	23,641	6411	22.03
A08W	4,208,284	188,712	0.013	0.006	44,753	6926	93.15
A09I	6,850,560	230,744	0.016	0.006	50,290	6710	153.87
A10W	1,403,568	105,485	0.01	0.006	29,316	6806	32.24
A11S	2,355,324	153,699	0.012	0.007	36,254	6797	50.5
A12S	2,224,370	194,901	0.012	0.007	39,005	6599	38.43
B07N	6,315,512	270,497	0.015	0.006	50,836	6776	132.11
B08W	3,224,481	152,315	0.011	0.006	38,488	6938	75.73
B09W	4,821,443	227,297	0.013	0.006	49,469	6873	107.54
B10W	2,246,679	123,018	0.011	0.006	32,260	6978	54.09
B11S	1,675,059	114,487	0.011	0.007	31,882	6589	35.9
B12S	2,823,683	140,521	0.012	0.006	37,261	6843	64.72
C07S	10,482,599	328,036	0.016	0.006	65,451	6621	219.94
C08I	1,051,320	100,553	0.01	0.007	25,978	6340	23.27
C09W	3,945,117	180,341	0.013	0.006	42,150	6935	91.99
C10N	1,060,648	94,092	0.01	0.007	25,254	6592	24.77
C11S	1,937,689	125,788	0.012	0.006	31,880	6815	43.75
C12S	479,412	60,756	0.009	0.007	16,586	4535	10.32
D07S	3,137,681	162,346	0.012	0.006	38,116	6809	72.13
D08W	1,127,041	85,710	0.01	0.006	25,476	6491	26.71
D09S	24,555	8580	0.012	0.006	883	208	0.2
D10N	814,774	77,508	0.01	0.006	22,223	6298	19.69
D11S	2,860,962	166,597	0.012	0.006	41,004	6818	60.81
D12S	476,212	58,172	0.011	0.007	16,603	4777	11.11
E07S	310,575	49,544	0.01	0.007	11,810	3427	5.73
E08I	2,329,405	156,765	0.011	0.006	36,697	6783	52.83
E09W	1,182,619	119,258	0.01	0.006	27,799	6354	23.22
E10S	1361,644	110,821	0.012	0.007	28,732	6665	28.6
E12W	701,654	79,193	0.01	0.006	21,530	5765	15.23
F07 N	2,413,712	138,285	0.011	0.006	33,944	6969	56.7
F08 W	1,735,184	114,265	0.011	0.006	30,603	6665	40.36
F09S	1,643,257	110,155	0.011	0.007	30,166	6733	37.7
F10 N	739,588	68,577	0.01	0.006	20,579	5869	16.84
F11S	1,542,460	98,117	0.01	0.006	28,884	6651	36.72
G07 N	3,845,340	171,087	0.013	0.006	40,668	6924	88.43
G08 W	1,637,683	115,971	0.011	0.006	31,144	6917	38.44
G09 W	675,273	68,986	0.01	0.006	20,229	5793	15.56
G10 N	2,277,786	128,426	0.011	0.006	32,260	6955	54.21
H06N	4,854,717	207,191	0.014	0.006	49,949	6919	107.4
H07S	3,731,409	192,342	0.012	0.006	46,340	6790	76.41
H08W	3,057,515	146,899	0.012	0.006	35,916	6936	71.65
H09W	1,579,956	107,146	0.01	0.006	28,594	6951	39.04
H10N	1,920,829	109,146	0.011	0.006	31,018	6942	46.4
H11S	1,530,490	103,703	0.01	0.006	29,508	6831	34.52
Mean	2,399,867	132,535	0.011	0.006	32,532	6371	53.43

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