Table 1 Statistics of sequenced data from eight different lanes.

Lane	Bases (G)	Total reads	Q30 (%)	Q20 (%)	R1 reads	R1 good barcode reads	R1 good ratio	R2 reads	R2 good barcode reads	R2 good ratio	Filter
L1	121	808 639 426	92	96	404 319 713	295 785 461	0.73	404 319 713	351 873 955	0.87	7
L2	125	832 928 728	93	97	416 464 364	295 646 345	0.71	416 464 364	357 060 282	0.86	5
L3	127	848 358 674	93	97	424 179 337	299 066 848	0.71	424 179 337	366 820 501	0.86	7
L4	144	961 606 222	93	97	480 803 111	404 804 456	0.84	480 803 111	413 407 380	0.86	3
L5	145	968 786 086	93	97	484 393 043	405 210 921	0.84	484 393 043	418 048 747	0.86	3
L6	142	948 387 596	92	97	474 193 798	402 730 494	0.85	474 193 798	418 114 080	0.88	3
L7	141	940 898 906	92	97	470 449 453	409 728 378	0.87	470 449 453	415 260 489	0.88	3
L8	142	948 527 654	92	97	474 263 827	403 069 787	0.85	474 263 827	414 036 702	0.87	3
Total	1 089	7 258 133 292	92.63	96.57	3 629 066 646	2 916 042 690	0.80	3 629 066 646	3 154 622 136	0.87	34

Eight libraries were constructed, with 96 samples per library, and a total of 768 samples were subjected to genotyping. Lanes 1–8 represent eight libraries. Bases refer to the amount of sequencing data. R1 reads and R2 reads refer to the reads for the paired end sequence (PE150). Total reads represents the sum of R1 reads and R2 reads. A good barcode read is a sequence read that matches one of the barcodes used in ddGBS. R1 good barcode reads and R2 good barcode reads refer to the good barcode reads for the paired end sequence (PE150). R1 good ratio = R1 good barcode reads/R1 reads. R2 good ratio = R2 good barcode reads/R2 reads. The filter refers to the number of filtered individuals.

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