Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	1,609,438	T→C	P126P (CCT→CCC)	yneJ →	LysR family transcriptional regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,609,438	0	T	C	100.0%	140.6 / NA	38	P126P (CCT→CCC)	yneJ	LysR family transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (14/24);  total (14/24)

CCGCTGCAGTGCGCATTCCAGCCACGCTGGCGGAATTCAACCGTCGTTATCCCAAAATTCAGTTTTCACTTTCCACCGGCCCTTCCGGCACTATGCTGGATGGTGTACTGGAGGGAAAACTGAATGCGGCGTTTATTGATGGACCCATTAACCATACTGCCATCGACGGG  >  NZ_CP009273/1609356‑1609525                                                                                   |                                                                                        ccGCTGCAGTGCGCATTCCAGCCACGCTGGCGGAATTCAACCGTCGTTATCCCAAAATTCAGTTTTCACTTTCCACCGGCCCCTCCGGCAc                                                                                 <  2:933240/91‑1 (MQ=255) ccGCTGCAGTGCGCATTCCAGCCACGCTGGCGGAATTCAACCGTCGTTATCCCAAAATTCAGTTTTCACTTTCCACCGGCCCCTCCGGCAc                                                                                 <  2:620501/91‑1 (MQ=255) ccGCTGCAGTGCGCATTCCAGCCACGCTGGCGGAATTCAACCGTCGTTATCCCAAAATTCAGTTTTCACTTTCCACCGGCCCCTCCGGCAc                                                                                 <  1:535723/91‑1 (MQ=255) ccGCTGCAGTGCGCATTCCAGCCACGCTGGCGGAATTCAACCGTCGTTATCCCAAAATTCAGTTTTCACTTTCCACCGGCCCCTCCGGCAc                                                                                 >  1:461124/1‑91 (MQ=255)   gCTGCAGTGCGCATTCCAGCCACGCTGGCGGAATTCAACCGTCGTTATCCCAAAATTCAGTTTTCACTTTCCACCGGCCCCTCCGGCACTa                                                                               <  2:104748/91‑1 (MQ=255)   gCTGCAGTGCGCATTCCAGCCACGCTGGCGGAATTCAACCGTCGTTATCCCAAAATTCAGTTTTCACTTTCCACCGGCCCCTCCGGCACTa                                                                               >  2:772372/1‑91 (MQ=255)   gCTGCAGTGCGCATTCCAGCCACGCTGGCGGAATTCAACCGTCGTTATCCCAAAATTCAGTTTTCACTTTCCACCGGCCCCTCCGGCACTa                                                                               >  1:35572/1‑91 (MQ=255)      gCAGTGCGCATTCCAGCCACGCTGGCGGAATTCAACCGTCGTTATCCCAAAATTCAGTTTTCACTTTCCACCGGCCCCTCCGGCACTATGc                                                                            <  1:165419/91‑1 (MQ=255)        aGTGCGCATTCCAGCCACGCTGGCGGAATTCAACCGTCGTTATCCCAAAATTCAGTTTTCACTTTCCACCGGCCCCTCCGGCACTATGCTg                                                                          <  2:240530/91‑1 (MQ=255)          tGCGCATTCCAGCCACGCTGGCGGAATTCAACCGTCGTTATCCCAAAATTCAGTTTTCACTTTCCACCGGCCCCTCCGGCACTATGCTGGa                                                                        <  1:384078/91‑1 (MQ=255)          tGCGCATTCCAGCCACGCTGGCGGAATTCAACCGTCGTTATCCCAAAATTCAGTTTTCACTTTCCACCGGCCCCTCCGGCACTATGCTGGa                                                                        <  1:606239/91‑1 (MQ=255)           gcgcATTCCAGCCACGCTGGCGGAATTCAACCGTCGTTATCCCAAAATTCAGTTTTCACTTTCCACCGGCCCCTCCGGCACTATGCTGGAt                                                                       <  2:702183/91‑1 (MQ=255)           gcgcATTCCAGCCACGCTGGCGGAATTCAACCGTCGTTATCCCAAAATTCAGTTTTCACTTTCCACCGGCCCCTCCGGCACTATGCTGGAt                                                                       <  2:913157/91‑1 (MQ=255)           gcgcATTCCAGCCACGCTGGCGGAATTCAACCGTCGTTATCCCAAAATTCAGTTTTCACTTTCCACCGGCCCCTCCGGCACTATGCTGGAt                                                                       <  2:35572/91‑1 (MQ=255)           gcgcATTCCAGCCACGCTGGCGGAATTCAACCGTCGTTATCCCAAAATTCAGTTTTCACTTTCCACCGGCCCCTCCGGCACTATGCTGGAt                                                                       >  1:748483/1‑91 (MQ=255)           gcgcATTCCAGCCACGCTGGCGGAATTCAACCGTCGTTATCCCAAAATTCAGTTTTCACTTTCCACCGGCCCCTCCGGCACTATGCTGGAt                                                                       <  1:836153/91‑1 (MQ=255)           gcgcATTCCAGCCACGCTGGCGGAATTCAACCGTCGTTATCCCAAAATTCAGTTTTCACTTTCCACCGGCCCCTCCGGCACTATGCTGGAt                                                                       <  1:880016/91‑1 (MQ=255)                ttCCAGCCACGCTGGCGGAATTCAACCGTCGTTATCCCAAAATTCAGTTTTCACTTTCCACCGGCCCCTCCGGCACTa                                                                               <  2:642744/78‑1 (MQ=255)                ttCCAGCCACGCTGGCGGAATTCAACCGTCGTTATCCCAAAATTCAGTTTTCACTTTCCACCGGCCCCTCCGGCACTa                                                                               >  1:642744/1‑78 (MQ=255)                     gCCACGCTGGCGGAATTCAACCGTCGTTATCCCAAAATTCAGTTTTCACTTTCCACCGGCCCCTCCGGCACTATGCTGGATGGTGTACTgg                                                             >  2:263115/1‑91 (MQ=255)                        aCGCTGGCGGAATTCAACCGTCGTTATCCCAAAATTCAGTTTTCACTTTCCACCGGCCCCTCCGGCACTATGCTGGATGGTGTACTGGAgg                                                          >  2:1043774/1‑91 (MQ=255)                          gCTGGCGGAATTCAACCGTCGTTATCCCAAAATTCAGTTTTCACTTTCCACCGGCCCCTCCGGCACTATGCTGGATGGTGTACTGGAGGGa                                                        >  1:705516/1‑91 (MQ=255)                          gCTGGCGGAATTCAACCGTCGTTATCCCAAAATTCAGTTTTCACTTTCCACCGGCACCTCCGGCACTATGCTGGATGGTGTACTGGAGGGa                                                        >  2:336222/1‑91 (MQ=255)                                       aaCCGTCGTTATCCCAAAATTCAGTTTTCACTTTCCACCGGCCCCTCCGGCACTATGCTGGATGGTGTACTGGAGGGAAAACTGAATgcgg                                           >  2:727886/1‑91 (MQ=255)                                        aCCGTCGTTATCCCAAAATTCAGTTTTCACTTTCCACCGGCCCCTCCGGCACTATGCTGGATGGTGTACTGGAGGGAAAACTGAATgcggc                                          <  2:162415/91‑1 (MQ=255)                                             cgtTATCCCAAAATTCAGTTTTCACTTTCCACCGGCCCCTCCGGCACTATGCTGGATGGTGTACTGGAGGGAAAACTGAATGCGGCGTTTa                                     >  1:11901/1‑91 (MQ=255)                                                    ccAAAATTCAGTTTTCACTTTCCACCGGCCCCTCCGGCACTATGCTGGATGGTGTACTGGAGGGAAAACTGAATGCGGCGTTTATTGATgg                              <  2:499088/91‑1 (MQ=255)                                                    ccAAAATTCAGTTTTCACTTTCCACCGGCCCCTCCGGCACTATGCTGGATGGTGTACTGGAGGGAAAACTGAATGCGGCGTTTATTGATgg                              <  1:891260/91‑1 (MQ=255)                                                     cAAAATTCAGTTTTCACTTTCCACCGGCCCCTCCGGCACTATGCTGGATGGTGTACTGGAGGGAAAACTGAATGCGGCGTTTATTGATGGa                             <  1:701582/91‑1 (MQ=255)                                                      aaaaTTCAGTTTTCACTTTCCACCGGCCCCTCCGGCAc                                                                                 <  2:242504/38‑1 (MQ=38)                                                      aaaaTTCAGTTTTCACTTTCCACCGGCCCCTCCGGCAc                                                                                 >  1:242504/1‑38 (MQ=38)                                                      aaaaTTCAGTTTTCACTTTCCACCGGCCCCTCCGGCACTATGCTGGATGGTGTACTGGAGGGAAAACTGAATGCGGCGTTTATTGATGGAc                            <  1:452834/91‑1 (MQ=255)                                                      aaaaTTCAGTTTTCACTTTCCACCGGCCCCTCCGGCACTATGCTGGATGGTGTACTGGAGGGAAAACTGAATGCGGCGTTTATTGATGGAc                            >  2:169961/1‑91 (MQ=255)                                                       aaaTTCAGTTTTCACTTTCCACCGGCCCCTCCGGCACTATGCTGGATGGTGTACTGGAGGGAAAACTGAATGCGGCGTTTATTGATGGAcc                           <  1:414891/91‑1 (MQ=255)                                                            cAGTTTTCACTTTCCACCGGCCCCTCCGGCACTATGCTGGATGGTGTACTGGAGGGAAAACTGAATgc                                             >  2:160409/1‑68 (MQ=255)                                                            cAGTTTTCACTTTCCACCGGCCCCTCCGGCACTATGCTGGATGGTGTACTGGAGGGAAAACTGAATgc                                             <  1:160409/68‑1 (MQ=255)                                                                   cACTTTCCACCGGCCCCTCCGGCACTATGCTGGATGGTGTACTGGAGGGAAAACTGAATGCGGCGTTTATTGATGGACCCATTAACCATAc               <  2:431630/91‑1 (MQ=255)                                                                               gCCCCTCCGGCACTATGCTGGATGGTGTACTGGAGGGAAAACTGAATGCGGCGTTTATTGATGGACCCATTAACCATACTGCCATCGACgg   <  2:748483/91‑1 (MQ=255)                                                                                ccccTCCGGCACTATGCTGGATGGTGTACTGGAGGGAAAACTGAATGCGGCGTTTATTGATGGACCCATTAACCATACTGCCATCGACggg  <  1:640079/91‑1 (MQ=255)                                                                                   |                                                                                        CCGCTGCAGTGCGCATTCCAGCCACGCTGGCGGAATTCAACCGTCGTTATCCCAAAATTCAGTTTTCACTTTCCACCGGCCCTTCCGGCACTATGCTGGATGGTGTACTGGAGGGAAAACTGAATGCGGCGTTTATTGATGGACCCATTAACCATACTGCCATCGACGGG  >  NZ_CP009273/1609356‑1609525

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑