Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
MC JC	NZ_CP009273	2,399,465	Δ7 bp	coding (650‑656/939 nt)	lrhA ←	transcriptional regulator LrhA

Missing coverage evidence...
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	NZ_CP009273	2399465	2399471	7	58 [0]	[0] 58	lrhA	transcriptional regulator LrhA

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NZ_CP009273	= 2399464	0 (0.000)	58 (1.220)	35/160	0.2	100%	coding (657/939 nt)	lrhA	transcriptional regulator LrhA
	?	NZ_CP009273	2399472 =	0 (0.000)					coding (649/939 nt)	lrhA	transcriptional regulator LrhA

GTCCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGGCGACATAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATACAAGA  >  NZ_CP009273/2399383‑2399557                                                                                          |                                                                                      cacgcaggtccgggctcatcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgaga                                                                                       >  2:1319089‑M2/90‑90 (MQ=255)  acgcaggtccgggctcatcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagaa                                                                                      >  2:828256‑M2/89‑90 (MQ=255)   cgcaggtccgggctcatcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAg                                                                                     >  1:118236‑M2/88‑90 (MQ=255)         tccgggctcatcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTc                                                                               <  1:828256‑M2/9‑1 (MQ=255)         tccgggctcatcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTc                                                                               <  2:118236‑M2/9‑1 (MQ=255)            gggctcatcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGcc                                                                            <  1:910598‑M2/12‑1 (MQ=255)              gctcatcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCAt                                                                          <  1:714475‑M2/14‑1 (MQ=255)                 catcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGa                                                                       >  2:340238‑M2/74‑90 (MQ=255)                 catcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGa                                                                       >  1:835508‑M2/74‑90 (MQ=255)                  atcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGaa                                                                      >  2:1307129‑M2/73‑90 (MQ=255)                    catctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAata                                                                    <  2:451878‑M2/20‑1 (MQ=255)                      tctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATc                                                                  <  1:897206‑M2/22‑1 (MQ=255)                      tctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATc                                                                  <  1:328183‑M2/22‑1 (MQ=255)                         caaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGc                                                               <  1:1483833‑M2/25‑1 (MQ=255)                         caaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagagtcgagAAGCCAGTCGCCATGGAATATCTGc                                                               <  1:865514‑M2/25‑1 (MQ=255)                           accggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCtt                                                             >  1:894297‑M2/64‑90 (MQ=255)                           accggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCtt                                                             <  1:340238‑M2/27‑1 (MQ=255)                           accggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCtt                                                             >  1:1029464‑M2/64‑90 (MQ=255)                              ggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTttat                                                          >  2:1498511‑M2/61‑90 (MQ=255)                              ggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTttat                                                          >  1:1044478‑M2/61‑90 (MQ=255)                               gccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGcc                                                                            <  1:417745‑M2/12‑1 (MQ=255)                               gccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGcc                                                                            >  2:417745‑M2/60‑71 (MQ=255)                                ccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTttatta                                                        >  2:366597‑M2/59‑90 (MQ=255)                                   tgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGc                                                     >  1:1357967‑M2/56‑90 (MQ=255)                                       gtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCg                                                 <  2:1029464‑M2/39‑1 (MQ=255)                                        tcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGc                                                >  1:937379‑M2/51‑90 (MQ=255)                                         cacgccacgcccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGcc                                               <  1:447769‑M2/41‑1 (MQ=255)                                         cacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCtt                                                             >  1:799162‑M2/50‑76 (MQ=255)                                         cacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCtt                                                             <  2:799162‑M2/27‑1 (MQ=255)                                         cacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGcc                                               <  2:305081‑M2/41‑1 (MQ=255)                                         cacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGcc                                               >  2:924894‑M2/50‑90 (MQ=255)                                              caagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCAc                                          <  2:937379‑M2/46‑1 (MQ=255)                                              caagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCAc                                          <  1:1370523‑M2/46‑1 (MQ=255)                                                agaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCa                                        <  1:240324‑M2/48‑1 (MQ=255)                                                   ccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCatat                                     >  2:273768‑M2/40‑90 (MQ=255)                                                     ggctttcactgccggacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATc                                                                  >  1:390690‑M2/38‑59 (MQ=255)                                                     ggctttcactgccggacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATc                                                                  <  2:390690‑M2/22‑1 (MQ=255)                                                     ggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATcg                                   >  1:1360864‑M2/38‑90 (MQ=255)                                                     ggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATcg                                   >  1:213141‑M2/38‑90 (MQ=255)                                                          tcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGaaa                              <  1:1307129‑M2/58‑1 (MQ=255)                                                           cactgtcgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAAc                             >  2:203636‑M2/32‑90 (MQ=255)                                                           cactgtcgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAAc                             <  1:203636‑M2/59‑1 (MQ=255)                                                           cactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGGGAAAc                             <  2:738812‑M2/59‑1 (MQ=255)                                                           cactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAAc                             <  1:759995‑M2/59‑1 (MQ=255)                                                           cactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAAc                             <  1:366597‑M2/59‑1 (MQ=255)                                                           cactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAAc                             <  2:132556‑M2/59‑1 (MQ=255)                                                           cactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAAc                             <  1:169599‑M2/59‑1 (MQ=255)                                                               gccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGcc                                               >  2:207570‑M2/28‑68 (MQ=255)                                                               gccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAAc                             >  2:849389‑M2/28‑86 (MQ=255)                                                               gccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAAc                             <  1:849389‑M2/59‑1 (MQ=255)                                                               gccgcacgaacgcccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGcc                                               <  1:207570‑M2/41‑1 (MQ=255)                                                                   cacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGGCGCCAGCACCATATCGCGAAACGGGCTAgg                     <  1:1073895‑M2/67‑1 (MQ=255)                                                                       aacggccggaatcgtcgagAATCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAAc                             >  1:1122616‑M2/20‑78 (MQ=255)                                                                       aacggccggaatcgtcgagAATCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAAc                             <  2:1122616‑M2/59‑1 (MQ=255)                                                                           gccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCa             <  2:215179‑M2/75‑1 (MQ=255)                                                                             cggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCACGAAACGGGCTAGGATCATCCAGc           <  2:835508‑M2/77‑1 (MQ=255)                                                                              ggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCa          <  2:431430‑M2/78‑1 (MQ=255)                                                                                      cgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATACAaga  <  2:1044478‑M2/86‑1 (MQ=255)                                                                                          |                                                                                      GTCCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGGCGACATAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATACAAGA  >  NZ_CP009273/2399383‑2399557

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑