Table 2.

Summary of reads generated by RNA-seq for each sample.

Sample	Raw reads	Clean reads	Overall aligned reads	Overall alignment rate
3	31,972,032	31,752,754	27,232,317	85.76%
4	29,101,802	28,323,384	25,108,913	88.65%
26	23,346,692	22,442,240	17,732,522	79.01%
8	28,812,098	27,209,832	21,958,483	80.70%
9	22,150,968	19,975,018	16,079,228	80.50%
14	33,766,962	32,350,232	24,801,434	76.67%

Sample numbers 3, 4, and 26 represent ALV-J- negative chickens; 8, 9, and 14 represent ALV-J- positive chickens.