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%	60.5 / NA	19	P126P (CCT→CCC)	yneJ	LysR family transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (3/16);  total (3/16)

TTGTCGCTGGCGATGAGCCGCAAGGTTTATTTTCTCTTGGTTCGCTGGAAAGCACCGCTGCAGTGCGCATTCCAGCCACGCTGGCGGAATTCAACCGTCGTTATCCCAAAATTCAGTTTTCACTTTCCACCGGCCCTTCCGGCACTATGCTGGATGGTGTACTGGAGGGAAAACTGAATGCGGCGTTTATTGATGGACCCATTAACCATACTGCCATCGACGGGATACCGGTATACCGCGAGGAACTGATGATCGT  >  NZ_CP009273/1609302‑1609557                                                                                                                                         |                                                                                                                        ttGTCGCTGGCGATGAGCCGCAAGGTTTATTTTCTCTTGGTTCGCTGGAAAGCACCGCTGCAGTGCGCATTCCAGCCACGCTGGCGGAATTCAACCGTCGTTATCCCAAAATTCAGTTTTCACTTTCCACCGGCCCCTc                                                                                                                       <  2:548980/139‑1 (MQ=255) ttGTCGCTGGCGATGAGCCGCAAGGTTTATTTTCTCTTGGTTCGCTGGAAAGCACCGCTGCAGTGCGCATTCCAGCCACGCTGGCGGAATTCAACCGTCGTTATCCCAAAATTCAGTTTTCACTTTCCACCGGCCCCTc                                                                                                                       <  1:294600/139‑1 (MQ=255)      gCTGGCGATGAGCCGCAAGGTTTATTTTCTCTTGGTTCGCTGGAAAGCACCGCTGCAGTGCGCATTCCAGCCACGCTGGCGGAATTCAACCGTCGTTATCCCAAAATTCAGTTTTCACTTTCCACCGGCCCCTCCGGCa                                                                                                                  <  2:71646/139‑1 (MQ=255)             aTGAGCCGCAAGGTTTATTTTCTCTTGGTTCGCTGGAAAGCACCGCTGCAGTGCGCATTCCAGCCACGCTGGCGGAATTCAACCGTCGTTATCCCAAAATTCAGTTTTCACTTTCCACCGGCCCCTCCGGCACTATGCt                                                                                                           <  2:104085/139‑1 (MQ=255)                aGCCGCAAGGTTTATTTTCTCTTGGTTCGCTGGAAAGCACCGCTGCAGTGCGCATTCCAGCCACGCTGGCGGAATTCAACCGTCGTTATCCCAAAATTCAGTTTTCACTTTCCACCGGCCCCTCCGGCACTATGCTGGa                                                                                                        <  2:35568/139‑1 (MQ=255)                                            gCTGGAAAGCACCGCTGCAGTGCGCATTCCAGCCACGCTGGCGGAATTCAACCGTCGTTATCCCAAAATTCAGTTTTCACTTTCCACCGGCCCCTCCGGCACTATGCTGGATGGTGTACTGGAGGGAAAACTGAATgc                                                                             <  2:517166/138‑1 (MQ=255)                                             cTGGAAAGCACCGCTGCAGTGCGCATTCCAGCCACGCTGGCGGAATTCAACCGTCGTTATCCCAAAATTCAGTTTTCACTTTCCACCGGCCCCTCCGGCACTATGCTGGATGGTGTACTGGAGGGAAAACTGAATgcgg                                                                           >  1:539426/1‑139 (MQ=255)                                                        cGCTGCAGTGCGCATTCCAGCCACGCTGGCGGAATTCAACCGTCGTTATCCCAAAATTCAGTTTTCACTTTCCACCGGCCCCTCCGGCACTATGCTGGa                                                                                                        <  1:260850/99‑1 (MQ=255)                                                        cGCTGCAGTGCGCATTCCAGCCACGCTGGCGGAATTCAACCGTCGTTATCCCAAAATTCAGTTTTCACTTTCCACCGGCCCCTCCGGCACTATGCTGGa                                                                                                        >  2:260850/1‑99 (MQ=255)                                                         gCTGCAGTGCGTATTCCAGTCACGCTGGCGGAATTCAACCGTCGTTATCCCAAAATTCAGTTTTCACTTTCCACCGGCCCCTCCGGCATTATGCTGGATGGTGTACTGGAGGGAAATCTGAATGCGGCGTTTATTGATg                                                               <  2:190897/139‑1 (MQ=255)                                                          cTGCAGTGCGCATTCCAGCCACGCTGGCGGAATTCAACCGTCGTTATCCCAAAATTCAGTTTTCACTTTCCACCGGCCCCTCCGGCACTATGCTGGATGGTGTACTGGAGGGAAAACTGAATGCGGCGTTTATTGATgg                                                              <  2:548788/139‑1 (MQ=255)                                                                          aGCCACGCTGGCGGAATTCAACCGTCGTTATCCCAAAATTCAGTTTTCACTTTCCACCGGCCCCTCCGGCa                                                                                                                  <  2:267705/71‑1 (MQ=255)                                                                          aGCCACGCTGGCGGAATTCAACCGTCGTTATCCCAAAATTCAGTTTTCACTTTCCACCGGCCCCTCCGGCa                                                                                                                  >  1:267705/1‑71 (MQ=255)                                                                                       gAATTCAACCGTCGTTATCCCAAAATTCAGTTTTCACTTTCCACCGGCCCCTCCGGCACTATGCTGGATGGTGTACTGGAGGGAAAACTGAATGCGGCGTTTATTGATGGACCCATTAACCATACTGCCATCGACGGGa                                 <  1:1083/139‑1 (MQ=255)                                                                                         aTTCAACCGTCGTTATCCCAAAATTCAGTTTTCACTTTCCACCGGCCCCTCCGGCACTATGCTGGATGGTGTACTGGAGGGAAAACTGAATGCGGCGTTTATTGATGGACCCATTAACCATACTGCCATCGACGGGAtc                               <  1:66163/139‑2 (MQ=255)                                                                                                 gtcgtTATCCCAAAATTCAGTTTTCACTTTCCACCGGCCCCTCCGGCACTATGCTGGATGGTGTACTGGAGGGAAAACTGAATGCGGCGTTTATTGATGGACCCATTAACCATACTGCCATCGACGGGATCCCGGtata                       <  1:341301/139‑1 (MQ=255)                                                                                                       aTCCCAAAATTCAGTTTTCACTTTCCACCGGCCCCTCCGGCACTATGCTGGATGGTGTACTGGAGGGAAAACTGAATGCGGCGTTTATTGATGGACCCATTAACCATACTGCCATCGACGGGATCCCGGTATACcgcg                  <  1:311569/138‑1 (MQ=255)                                                                                                                     ttttCACTTTCCACCGCCCCCTCCGGCACTATGCTGGATGGTGTACTGGAGGGAAAACTGAATGCGGCGTTTATTGATGGACCCATTAACCATACTGCCATCGACGGGATCCCGGTATACCGCGAGGAACTGATGATCg   <  2:141239/139‑1 (MQ=255)                                                                                                                       ttCACTTTCCACCGGCCCCTCCGGCACTATGCTGGATGGTGTACTGGAGGGAAAACTGAATGCGGCGTTTATTGATGGACCCATTAACCATACTGCCATCGACGGGATCCCGGTATACCGCGAGGAACTGATGATCGt  <  2:539426/138‑1 (MQ=255)                                                                                                                                         |                                                                                                                        TTGTCGCTGGCGATGAGCCGCAAGGTTTATTTTCTCTTGGTTCGCTGGAAAGCACCGCTGCAGTGCGCATTCCAGCCACGCTGGCGGAATTCAACCGTCGTTATCCCAAAATTCAGTTTTCACTTTCCACCGGCCCTTCCGGCACTATGCTGGATGGTGTACTGGAGGGAAAACTGAATGCGGCGTTTATTGATGGACCCATTAACCATACTGCCATCGACGGGATACCGGTATACCGCGAGGAACTGATGATCGT  >  NZ_CP009273/1609302‑1609557

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑