Missing coverage evidence...
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	W3110S.gb	1653366	1653460	95	38 [0]	[0] 32	intQ	predicted defective integrase

TCATCAAAAATATCCTGAGCATAATCGGTGAAAAAAATCTTGCCTCATCGATTAATAAAGAAAAA  >  W3110S.gb/1653461‑1653525 |                                                                 tcatcaAAAATATCCTGAGCATAATCGGTGAAAAAAATCTTGCCTCATCGATTAATAAAGaataa  <  1:242798/65‑1 (MQ=255) tcatcaAAAATATCCTGAGCATAATCGGTGAAAAAAATCTTGCCTCATCGATTAATAAAGaaaaa  <  1:1835596/65‑1 (MQ=255) tcatcaAAAATATCCTGAGCATAATCGGTGAAAAAAATCTTGCCTCATCGATTAATAAAGaaaaa  <  1:998823/65‑1 (MQ=255) tcatcaAAAATATCCTGAGCATAATCGGTGAAAAAAATCTTGCCTCATCGATTAATAAAGaaaaa  <  1:977334/65‑1 (MQ=255) tcatcaAAAATATCCTGAGCATAATCGGTGAAAAAAATCTTGCCTCATCGATTAATAAAGaaaaa  <  1:963612/65‑1 (MQ=255) tcatcaAAAATATCCTGAGCATAATCGGTGAAAAAAATCTTGCCTCATCGATTAATAAAGaaaaa  <  1:922220/65‑1 (MQ=255) tcatcaAAAATATCCTGAGCATAATCGGTGAAAAAAATCTTGCCTCATCGATTAATAAAGaaaaa  <  1:868499/65‑1 (MQ=255) tcatcaAAAATATCCTGAGCATAATCGGTGAAAAAAATCTTGCCTCATCGATTAATAAAGaaaaa  <  1:84587/65‑1 (MQ=255) tcatcaAAAATATCCTGAGCATAATCGGTGAAAAAAATCTTGCCTCATCGATTAATAAAGaaaaa  <  1:688346/65‑1 (MQ=255) tcatcaAAAATATCCTGAGCATAATCGGTGAAAAAAATCTTGCCTCATCGATTAATAAAGaaaaa  <  1:639907/65‑1 (MQ=255) tcatcaAAAATATCCTGAGCATAATCGGTGAAAAAAATCTTGCCTCATCGATTAATAAAGaaaaa  <  1:390372/65‑1 (MQ=255) tcatcaAAAATATCCTGAGCATAATCGGTGAAAAAAATCTTGCCTCATCGATTAATAAAGaaaaa  <  1:344982/65‑1 (MQ=255) tcatcaAAAATATCCTGAGCATAATCGGTGAAAAAAATCTTGCCTCATCGATTAATAAAGaaaaa  <  1:331018/65‑1 (MQ=255) tcatcaAAAATATCCTGAGCATAATCGGTGAAAAAAATCTTGCCTCATCGATTAATAAAGaaaaa  <  1:328899/65‑1 (MQ=255) tcatcaAAAATATCCTGAGCATAATCGGTGAAAAAAATCTTGCCTCATCGATTAATAAAGaaaaa  <  1:1886916/65‑1 (MQ=255) tcatcaAAAATATCCTGAGCATAATCGGTGAAAAAAATCTTGCCTCATCGATTAATAAAGaaaaa  <  1:1866795/65‑1 (MQ=255) tcatcaAAAATATCCTGAGCATAATCGGTGAAAAAAATCTTGCCTCATCGATTAATAAAGaaaaa  <  1:1041880/65‑1 (MQ=255) tcatcaAAAATATCCTGAGCATAATCGGTGAAAAAAATCTTGCCTCATCGATTAATAAAGaaaaa  <  1:1832596/65‑1 (MQ=255) tcatcaAAAATATCCTGAGCATAATCGGTGAAAAAAATCTTGCCTCATCGATTAATAAAGaaaaa  <  1:1779065/65‑1 (MQ=255) tcatcaAAAATATCCTGAGCATAATCGGTGAAAAAAATCTTGCCTCATCGATTAATAAAGaaaaa  <  1:1660021/65‑1 (MQ=255) tcatcaAAAATATCCTGAGCATAATCGGTGAAAAAAATCTTGCCTCATCGATTAATAAAGaaaaa  <  1:1658945/65‑1 (MQ=255) tcatcaAAAATATCCTGAGCATAATCGGTGAAAAAAATCTTGCCTCATCGATTAATAAAGaaaaa  <  1:1625979/65‑1 (MQ=255) tcatcaAAAATATCCTGAGCATAATCGGTGAAAAAAATCTTGCCTCATCGATTAATAAAGaaaaa  <  1:1548104/65‑1 (MQ=255) tcatcaAAAATATCCTGAGCATAATCGGTGAAAAAAATCTTGCCTCATCGATTAATAAAGaaaaa  <  1:128622/65‑1 (MQ=255) tcatcaAAAATATCCTGAGCATAATCGGTGAAAAAAATCTTGCCTCATCGATTAATAAAGaaaaa  <  1:1266778/65‑1 (MQ=255) tcatcaAAAATATCCTGAGCATAATCGGTGAAAAAAATCTTGCCTCATCGATTAATAAAGaaaaa  <  1:1222532/65‑1 (MQ=255) tcatcaAAAATATCCTGAGCATAATCGGTGAAAAAAATCTTGCCTCATCGATTAATAAAGaaaaa  <  1:1198981/65‑1 (MQ=255) tcatcaAAAATATCCTGAGCATAATCGGTGAAAAAAATCTTGCCTCATCGATTAATAAAGaaaaa  <  1:111328/65‑1 (MQ=255) tcatcaAAAATATCCTGAGCATAATCGGTGAAAAAAATCTTGCCTCATCGATTAATAAAGaaaaa  <  1:1108352/65‑1 (MQ=255) tcatcaAAAATATCCTGAGCATAATCGGTGAAAAAAATCTTGCCTCATCGATTAATAAAGaaaaa  <  1:1069966/65‑1 (MQ=255) tcatcaAAAATATCCTGAGCATAATCGGTGAAAAAAATCTTGCCTCATCGATTAATAAAGaaaaa  <  1:105968/65‑1 (MQ=255) tcatcaAAAATATCCTGAGCATAATCGGTGAAAAAAATCTTGCCTCATCGATTAATAAAGaaaaa  <  1:1053413/65‑1 (MQ=255) |                                                                 TCATCAAAAATATCCTGAGCATAATCGGTGAAAAAAATCTTGCCTCATCGATTAATAAAGAAAAA  >  W3110S.gb/1653461‑1653525

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑