Table 2. RNA-seq read mapping summary.

Sample	PRO1	PRO2	PRO3	AXA1	AXA2	AXA3	AMA1	AMA2	AMA3
Random primed library
Total paired-end reads	12,835,963	13,087,624	12,858,646	13,124,114	13,748,422	12,778,984	13,477,640	13,357,246	13,044,810
Low-quality reads	20,538	23,558	29,575	17,061	34,371	17,891	9,434	13,357	11,740
Reads mapping to multiple loci	4,133,727	3,572,451	4,109,315	5,155,858	4,552,037	4,044,110	1,187,608	2,910,706	3,115,683
Genes with non zero read counts	9,129	9,119	9,119	9,133	9,129	9,125	9,112	9,123	9,123
Total reads mapped to L. mexicana genome	12,220,790	12,301,132	12,109,395	12,525,089	12,950,160	11,893,323	3,437,982	7,224,190	7,767,651
Reads with no match in genome	594,635	762,934	719,676	581,964	763,891	867,770	10,030,224	6,119,699	5,265,419
Total reads with SL sequence (last 12nt)	673,297	1,067,867	937,353	786,722	1,009,393	1,225,884	262,651	499,028	572,112
Mapped reads with SL sequence (last 12nt)	665,046	1,051,560	923,254	778,432	994,815	1,208,732	259,961	493,948	566,435
T15VN PRIMED LIBRARY
Total reads	nd	25,956,366	22,854,437	nd	21,935,789	20,450,384	nd	23,956,594	25,696,946
Low-quality reads	nd	8,012,973	8,617,839	nd	6,910,070	5,436,250	nd	9,613,243	8,996,465
Total reads with poly(A) tail (≥5 A)	nd	2,097,561	2,088,542	nd	2,200,926	2,149,944	nd	1,793,186	1,476,286
Mapped reads with poly(A) tail (≥5 A)	nd	756,459	767,004	nd	805,680	812,005	nd	424,491	373,912