Table 1.

Sequence and mapping statistics for raw Illumina data

Strain	Treatment	Repeat	Total reads	No. mapped	% mapped	Properly paired	% properly paired	Singletons	% singletons	Unique reads in ensembl v58 annotations	% unique reads in ensembl v58 annotations
BALB/c	Infected	1	35 646 760	24 026 742	67.4	18 883 064	78.59	3 802 882	15.83	13 914 673	57.9
BALB/c	Infected	2	39 663 694	26 450 844	73.3	21 349 672	80.71	4 071 578	15.39	15 261 028	57.7
BALB/c	Infected	3	40 960 176	26 670 826	65.1	20 637 676	77.38	4 486 602	16.82	15 578 573	58.4
BALB/c	Thio	1	40 398 232	26 011 652	64.3	21 817 520	83.88	3 454 426	13.28	14 732 920	56.6
BALB/c	Thio	2	48 366 774	33 194 643	68.6	26 782 502	80.68	5 494 173	16.55	19 344 275	58.2
BALB/c	Thio	3	45 552 296	28 796 129	63.2	24 350 132	84.56	4 167 411	14.47	16 480 896	57.2
IL4Rα−/−	Infected	1	56 700 552	31 428 896	55.4	27 125 044	86.31	4 172 298	13.28	17 799 754	56.6
IL4Rα−/−	Infected	2	23 150 358	15 076 797	65.1	12 977 824	86.08	1 911 075	12.68	8 493 659	56.3
IL4Rα−/−	Infected	3	60 376 960	42 872 365	71.0	32 888 162	76.71	6 826 787	15.92	24 849 426	57.9
IL4Rα−/−	Thio	1	40 492 838	24 144 541	59.6	19 772 782	81.89	3 547 653	14.69	13 845 966	57.3
IL4Rα−/−	Thio	2	22 996 482	13 033 134	56.7	8 952 742	68.69	2 418 168	18.55	7 725 619	59.2
IL4Rα−/−	Thio	3	36 062 844	19 911 073	55.2	14 751 228	74.09	3 874 775	19.46	11 892 859	59.7