Table 2.

Comparison results of clean sequences on reference genomes

Sample	Clean reads	Total mapped	Multiple mapped	Uniquely mapped	Reads map to +	Reads map to -	Non-splice reads	Splice reads
VA116	69282386	56937342 (82.18%)	1149403 (1.66%)	55787939 (80.52%)	27915758 (40.29%)	27872181 (40.23%)	39876131 (57.56%)	15911808 (22.97%)
Basma	76348022	63090417 (82.64%)	1516187 (1.99%)	61574230 (80.65%)	30785508 (40.32%)	30788722 (40.33%)	40938897 (53.62%)	20635333 (27.03%)
F1	66926392	53935066 (80.59%)	1303116 (1.95%)	52631950 (78.64%)	26330586 (39.34%)	26301364 (39.3%)	34462915 (51.49%)	18169035 (27.15%)

(1) Total mapped represents the total amount of sequencing sequences that can be mapped to the genome. (2) Multiple mapped represents the total amount of sequencing sequences with multiple alignment positions on the reference sequence. (3) Uniquely mapped represents the total amount of sequencing sequences with unique alignment position on the reference sequence. (4) Reads map to ‘+’, Reads map to ‘-’ represent the number of sequencing sequence that aligne to positive and negative chains on the genome