Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP009273	3,547,518	G→A	E359K (GAA→AAA)	malT →	mal regulon transcriptional activator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	3,547,518	0	G	A	100.0%	107.4 / NA	31	E359K (GAA→AAA)	malT	mal regulon transcriptional activator
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (16/15);  total (16/15)

CGGCGGAGCTGCCGGAAATCCACCGTGCCGCCGCAGAAAGCTGGATGGCCCAGGGATTTCCCAGCGAAGCAATTCATCATGCGCTGGCGGCAGGCGATGCGCTGATGCTGCGCGATATTCTGCTTAAT  >  CP009273/3547453‑3547580                                                                  |                                                               cggcggAGCTGCCGGAAATCCACCGTGCCGCCGCAGAAAGCTGGATGGCCCAGGGATTTCCCAGCaaa                                                              <  1:1292391/68‑1 (MQ=255) cggcggAGCTGCCGGAAATCCACCGTGCCGCCGCAGAAAGCTGGATGGCCCAGGGATTTCCCAGCaaa                                                              <  1:1108811/68‑1 (MQ=255)   gcggAGCTGCCGGAAATCCACCGTGCCGCCGCAGAAAGCTGGATGGCCCAGGGATTTCCCAGCAAAGc                                                            <  1:985971/68‑1 (MQ=255)                  aTCCACCGTGCCGCCGCAGCAAGCTGGATGGCCCAGGGATTTCCCAGCAAAGCAATTCATCATGCGCt                                             >  1:5097389/1‑68 (MQ=255)                      aCCGTGCCGCCGCAGAAAGCTGGATGGCCCAGGGATTTCCCAGCAAAGCAATTCATCATGCGCTggcg                                         >  1:5362033/1‑68 (MQ=255)                           gccgccGCAGAAAGCTGGAAGGCCCAGGGAATTCCCAGCAAAGCAATTCATCATGCGCTGGCGGCAgg                                    >  1:2170509/1‑68 (MQ=255)                                 gcAGAAAGCTGGATGGCCCAGGGATTTCCCAGCAAAGCAATTCATCATGCGCTGGCGGCAGGCGATgc                              <  1:720316/68‑1 (MQ=255)                                 gcAGAAAGCTGGATGGCCCAGGGATTTCCCAGCAAAGCAATTCATCATGCGCTGGCGGCAGGCGATgc                              <  1:2186862/68‑1 (MQ=255)                                  cAGAAAGCTGGATGGCCCAGGGATTTCCCAGCAAAGCAATTCATCATGCGCTGGCGGCAGGCGATgcg                             <  1:59293/68‑1 (MQ=255)                                  cAGAAAGCTGGATGGCCCAGGGATTTCCCAGCAAAGCAATTCATCATGCGCTGGCGGCAGGCGATgcg                             <  1:1601964/68‑1 (MQ=255)                                  cAGAAAGCTGGATGGCCCAGGGATTTCCCAGCAAAGCAATTCATCATGCGCTGGCGGCAGGCGATgcg                             <  1:4161971/68‑1 (MQ=255)                                           ggATGGCCCAGGGATTTCCCAGCAAAGCAATTCATCATGCGCTGGCGGCAGGCGATGCGCTGAtgctg                    >  1:4387/1‑68 (MQ=255)                                            gATGGCCCAGGGAGTTCCCAGCAAAGCAAATCATCATGCGCTGGGGGCTGGCGTTGCGCTGAtgctgc                   <  1:5069500/68‑1 (MQ=255)                                              tGGCCCAGGGATTTCCCAGCAAAGCAATTCATCATGCGCTGGCGGCAGGCGATGCGCTGATGCTgcgc                 <  1:1179364/68‑1 (MQ=255)                                              tGGCCCAGGGATTTCCCAGCAAAGCAATTCATCATGCGCTGGCGGCAGGCGATGCGCTGATGCTgcgc                 >  1:779962/1‑68 (MQ=255)                                                 cccAGGGATTTCCCAGCAAAGCAATTCATCATGCGCTGGCGGCAGGCGATGCGCTGATGCTGCGCGat              <  1:2354492/68‑1 (MQ=255)                                                 cccAGGGATTTCCCAGCAAAGCAATTCATCATGCGCTGGCGGCAGGCGATGCGCTGATGCTGCGCGat              <  1:5262305/68‑1 (MQ=255)                                                 cccAGGGATTTCCCAGCAAAGCAATTCATCATGCGCTGGCGGCAGGCGATGCGCTGATGCTGCGCGat              <  1:4001856/68‑1 (MQ=255)                                                  ccAGGGATTTCCCAGCAAAGCAATTCATCATGCGCTGGCGGCAGGCGATGCGCTGATGCTGCGCGata             >  1:3752047/1‑68 (MQ=255)                                                      ggATTACCCAGCAAAGCAATTCATCATGCGCTGGCGGCAGGCGATGCGCTGATGCTGCGCGATATTCt         <  1:2155538/68‑1 (MQ=255)                                                       gATTTCCCAGCAAAGCAATTCATCATGCGCTGGCGGCAGGCGATGCGCTGATGCTGCGCGATATTCTg        >  1:4474323/1‑68 (MQ=255)                                                       gATTTCCCAGCAAAGCAATTCATCATGCGCTGGCGGCAGGCGATGCGCTGATGCTGCGCGATATTCTg        >  1:4560993/1‑68 (MQ=255)                                                       gATTTCCCAGCAAAGCAATTCATCATGCGCTGGCGGCAGGCGATGCGCTGATGCTGCGCGATATTCTg        >  1:4444623/1‑68 (MQ=255)                                                       gATTTCCCAGCAAAGCAATTCATCATGCGCTGGCGGCAGGCGATGCGCTGATGCTGCGCGATATTCTg        >  1:5132177/1‑68 (MQ=255)                                                       gATTTCCCAGCAAAGCAATTCATCATGCGCTGGCGGCAGGCGATGCGCTGATGCTGCGCGATATTCTg        >  1:4409194/1‑68 (MQ=255)                                                       gATTTCCCAGCAAAGCAATTCATCATGCGCTGGCGGCAGGCGATGCGCTGATGCTGCGCGATATTCTg        >  1:5334442/1‑68 (MQ=255)                                                       gATTTCCCAGCAAAGCAATTCATCATGCGCTGGCGGCAGGCGATGCGCTGATGCTGCGCGATATTCTg        >  1:1580360/1‑68 (MQ=255)                                                       gATTTCCCAGCAAAGCAATTCATCATGCGCTGGCGGCAGGCGATGCGCTGATGCTGCGCGATATTCTg        >  1:1519285/1‑68 (MQ=255)                                                       gATTTCCCAGCAAAGCAATTCATCATGCGCTGGCGGCAGGCGATGCGCTGATGCTGCGCGATATTCTg        <  1:7525/68‑1 (MQ=255)                                                       gATTTCCCAGCAAAGCAATTCATCATGCGCTGGCGGCAGGCGATGCGCTGATGCTGCGCGATATTCTg        <  1:3983424/68‑1 (MQ=255)                                                             ccAGCAAAGCAATTCATCATGCGCTGGCGGCAGGCGATGCGCTGATGCTGCGCGATATTCTGCTTAAt  <  1:4992256/68‑1 (MQ=255)                                                             ccAGCAAAGCAATTCATCATGCGCTGGCGGCAGGCGATGCGCTGATGCTGCGCGATATTCTGCTTAAt  >  1:1601319/1‑68 (MQ=255)                                                             ccAGCAAAGCAATTCATCATGCGCTGGCGGCAGGCGATGCGCTGATGCTGCGCGATATTCTGATTAAt  >  1:2607314/1‑68 (MQ=255)                                                                  |                                                               CGGCGGAGCTGCCGGAAATCCACCGTGCCGCCGCAGAAAGCTGGATGGCCCAGGGATTTCCCAGCGAAGCAATTCATCATGCGCTGGCGGCAGGCGATGCGCTGATGCTGCGCGATATTCTGCTTAAT  >  CP009273/3547453‑3547580

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: ‑