sample	Total reads processed	Reads with adapters	Reads that were too short	Reads written (passing filters)
KO_0h_replicate_II.log               21564095                  3883539 (18.0%)           3103286 (14.4%)    18460809 (85.6%)
KO_0h_replicate_I.log               21131300                  4121718 (19.5%)           4417860 (20.9%)    16713440 (79.1%)
KO_2h_replicate_II.log               22823028                  4744526 (20.8%)           4347703 (19.0%)    18475325 (81.0%)
KO_2h_replicate_I.log               38423575                 11990094 (31.2%)          12332044 (32.1%)    26091531 (67.9%)
KO_6h_replicate_II.log               34443861                 10064975 (29.2%)          10394096 (30.2%)    24049765 (69.8%)
KO_6h_replicate_I.log               25462277                  3603211 (14.2%)           4415080 (17.3%)    21047197 (82.7%)
KO_IFN-gamma_replicate_II.log               32460065                  8811383 (27.1%)           9193327 (28.3%)    23266738 (71.7%)
KO_IFN_replicate_I.log               42355116                  8267970 (19.5%)           8655595 (20.4%)    33699521 (79.6%)
KO_IL4_replicate_II.log               20943779                  6117687 (29.2%)           6314570 (30.2%)    14629209 (69.8%)
KO_IL4_replicate_I.log               18357940                  2742854 (14.9%)           3070769 (16.7%)    15287171 (83.3%)
WT_0h_replicate_II.log               31008530                 11838608 (38.2%)          12093898 (39.0%)    18914632 (61.0%)
WT_0h_replicate_I.log               45640751                 17161839 (37.6%)          17573802 (38.5%)    28066949 (61.5%)
WT_2h_replicate_II.log               52499204                 20976986 (40.0%)          21744683 (41.4%)    30754521 (58.6%)
WT_2h_replicate_I.log               39171661                 13620949 (34.8%)          13967258 (35.7%)    25204403 (64.3%)
WT_6h_replicate_II.log               31126332                  9381663 (30.1%)           9597650 (30.8%)    21528682 (69.2%)
WT_6h_replicate_I.log               15918777                  3069776 (19.3%)           3400847 (21.4%)    12517930 (78.6%)
WT_IFN-gamma_replicate_II.log               33594001                  8878771 (26.4%)           8986817 (26.8%)    24607184 (73.2%)
WT_IFN-gamma_replicate_I.log               23069391                  7209627 (31.3%)           6078758 (26.3%)    16990633 (73.7%)
WT_IL4_replicate_II.log               13132576                  2395704 (18.2%)           2639102 (20.1%)    10493474 (79.9%)
WT_IL4_replicate_I.log               18156532                  2846816 (15.7%)           2492142 (13.7%)    15664390 (86.3%)

sample                          Total reads	
KO_0h_replicate_II              21564095
KO_0h_replicate_I               21131300
KO_2h_replicate_II              22823028
KO_2h_replicate_I               38423575
KO_6h_replicate_II              34443861
KO_6h_replicate_I               25462277
KO_IFN-gamma_replicate_II       32460065
KO_IFN_replicate_I              42355116
KO_IL4_replicate_II             20943779
KO_IL4_replicate_I              18357940
WT_0h_replicate_II              31008530
WT_0h_replicate_I               45640751
WT_2h_replicate_II              52499204
WT_2h_replicate_I               39171661
WT_6h_replicate_II              31126332
WT_6h_replicate_I               15918777
WT_IFN-gamma_replicate_II       33594001
WT_IFN-gamma_replicate_I        23069391
WT_IL4_replicate_II             13132576
WT_IL4_replicate_I              18156532