Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	4,507,805	T→C	E83G (GAA→GGA)	fecI ←	RNA polymerase sigma factor FecI

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	4,507,805	0	T	C	100.0%	103.0 / NA	28	E83G (GAA→GGA)	fecI	RNA polymerase sigma factor FecI
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (16/12);  total (16/12)

AGGAGTTGTAGGGTCTCGAGTTGGCTTTCGCGTTCCTCAGGTGAAGGCGCTCCCCCCTCCGGCATAAGCGCCAGCATCTCCAGATACGCTTTTTCCAGCGCGTTTCGGCGAAACAGGTCCACCATCACGCGTTTGGCGATAGTGCAGAGGAAGGAGCGAGGATCGCGGATCGTCGAGAGCGTTTCGCTGACCATTACCCGCAAAAAAGTGTCCTGGGCAATGTCATC  >  NZ_CP009273/4507712‑4507938                                                                                              |                                                                                                                                      aggagTTGTAGGGTCTCGAGTTGGCTTTCGCGTTCCTCAGGTGAAGGCGCTCCCCCCTCCGGCATAAGCGCCAGCATCTCCAGATACGCTTTTCCCAGCGCGTTTCGGCGAAACAGGTCCACCATCACGCGTTTGGCGa                                                                                          <  1:49311/139‑1 (MQ=255)   gagTTGTAGGGTCTCGAGTTGGCTTTCGCGTTCCTCAGGTGAAGGCGCTCCCCCCTCCGGCATAAGCGCCAGCATCTCCAGATACGCTTTTCCCAGCGCGTTTCGGCGAAACAGGTCCACCATCACGCGTTTGGCGATa                                                                                        <  2:131318/139‑1 (MQ=255)        gTAGGGTCTCGAGTTGGCTTTCGCGTTCCTCCGGTGAAGGCGCTCCCCCCTCCGGCATAAGCGCCAGCATCTCCAGATACGCTTTTCCCAGCGCGTTTCGGCGAAACAGGTCCACCATCACGCGTTTGGCGa                                                                                          >  2:9522/1‑132 (MQ=255)        gTAGGGTCTCGAGTTGGCTTTCGCGTTCCTCAGGTGAAGGCGCTCCCCCCTCCGGCATAAGCGCCAGCATCTCCAGATACGCTTTTCCCAGCGCGTTTCGGCGAAACAGGTCCACCATCACGCGTTTGGCGa                                                                                          <  1:9522/132‑1 (MQ=255)              tctcGAGTTGGCTTTCGCGTTCCTCAGGTGAAGGCGCTCCCCCCTCCGGCATAAGCGCCAGCATCTCCAGATACGCTTTTCCCAGCGCGTTTCGGCGAAACAGGTCCACCATCACGCGTTTGGCGa                                                                                          <  2:378670/126‑1 (MQ=255)              tctcGAGTTGGCTTTCGCGTTCCTCAGGTGAAGGCGCTCCCCCCTCCGGCATAAGCGCCAGCATCTCCAGATACGCTTTTCCCAGCGCGTTTCGGCGAAACAGGTCCACCATCACGCGTTTGGCGa                                                                                          >  1:378670/1‑126 (MQ=255)                tcGAGTTGGCTTTCGCGTTCCTCAGGTGAAGGCGCTCCCCCCTCCGGCATAAGCGCCAGCATCTCCAGATACGCTTTTCCCAGCGCGTTTCGGCGAAACAGGTCCACCATCACGCGTTTGGCGATAGTGCAGaggaag                                                                            >  2:325530/1‑138 (MQ=255)                tcGAGTTGGCTTTCGCGTTCCTCAGGTGAAGGCGCTCCCCCCTCCGGCATAAGCGCCAGCATCTCCAGATACGCTTTTCCCAGCGCGTTTCGGCGAAACAGGTCCACCATCACGCGTTTGGCGATAGTGCAGagga                                                                              >  1:290969/1‑136 (MQ=255)                tcGAGTTGGCTTTCGCGTTCCTCAGGTGAAGGCGCTCCCCCCTCCGGCATAAGCGCCAGCATCTCCAGATACGCTTTTCCCAGCGCGTTTCGGCGAAACAGGTCCACCATCACGCGTTTGGCGATAGTGCAGagga                                                                              <  2:290969/136‑1 (MQ=255)                   aGTTGGCTTTCGCGTTCCTCAGGTGAAGGCGCTCCCCCCTCCGGCATAAGCGCCAGCATCTCCAGATACGCTTTTCCCAGCGCGTTTCGGCGAATCAGGTCCACCATCACGCGTTTGGCGATAGTGCAGAGGAAGGAGc                                                                        >  2:86421/1‑139 (MQ=255)                       ggCTTTCGCGTTCCTCAGGTGAAGGCGCTCCCCCCTCCGGCATAAGCGCCAGCATCTCCAGATACGCTTTTCCCAGCGCGTTTCGGCGAAACAGGTCCACCATCACGCGTTTGGCGATAGTGCAGAGGAAGGAGCGAg                                                                     >  2:200151/1‑138 (MQ=255)                            tCGCGTTCCTCAGGTGAAGGCGCTCCCCCCTCCGGCATAAGCGCCAGCATCTCCAGATACGCTTTTCCCAGCGCGTTTCGGCGAAACAGGTCCACCATCACGCGTTTGGCGATAGTGCAGAGGAAGGAGCGAGGATcgc                                                               >  2:360770/1‑139 (MQ=255)                            tCGCGTTCCTCAGGTGAAGGCGCTCCCCCCTCCGGCATAAGCGCCAGCATCTCCAGATACGCTTTTCCCAGCGCGTTTCGGCGAAACAGGTCCACCATCACGCGTTTGGCGATAGTGCAGAGGAAGGAGCGAGGATcgc                                                               >  2:280090/1‑139 (MQ=255)                                              ggCGCTCCCCCCTCCGGCATAAGCGCCAGCATCTCCAGATACGCTTTTCCCAGCGCGTTTCGGCGAAACAGGTCCACCATCACGCGTTTGGCGATAGTGCAGAGGAAGGAGCGAGGATCGCGGATCGTCGAGAGCGttt                                             >  2:112319/1‑139 (MQ=255)                                                cgcTCCCCCCTCCGGCATAAGCGCCAGCATCTCCAGATACGCTTTTCCCAGCGCGTTTCGGCGAAACAGGTCCACCATCACGCGTTTGGCGATAGTGCAGAGGAAGGAGCGAGGATCGCGGATCGTCGAGAGCGTTTCg                                           <  1:360770/139‑1 (MQ=255)                                                cgcTCCCCCCTCCGGCATAAGCGCCAGCATCTCCAGATACGCTTTTCCCAGCGCGTTTCGGCGAAACAGGTCCACCATCACGCGTTTGGCGATAGTGCAGAGGAAGGAGCGAGGATCGCGGATCGTCGAGAGCGTTTCg                                           <  1:280090/139‑1 (MQ=255)                                                   tCCCCCCTCCGGCATAAGCGCCAGCATCTCCAGATACGCTTTTCCCAGCGCGTTTCGGCGAAACAGGTCCACCATCACGCGTTTGGCGATAGTGCAGAGGAAGGAGCGAGGATCGCGGATCGTCGAGAGCGTTTCGCt                                         >  2:122130/1‑138 (MQ=255)                                                               cATAAGCGCCAGCATCTCCAGATACGCTTTTCCCAGCGCGTTTCGGCGAAACAGGTCCACCATCACGCGTTTGGCGATAGTGCAGAGGAAGGAGCGAGGATCGCGGATCGTCGAGAGCGTTTCGCTGACCATTACCCg                             >  1:40595/1‑138 (MQ=255)                                                                 tAAGCGCCAGCATCTCCAGATACGCTTTTCCCAGCGCGTTTCGGCGAAACAGGTCCACCATCACGCGTTTGGCGATAGTGCAGAGGAAGGAGCGAGGATCGCGGATCGTCGAGAGCGTTTCGCTGACCATTACCCGCa                           >  1:201220/1‑138 (MQ=255)                                                                 tAAGCGCCAGCATCTCCAGATACGCTTTTCCCAGCGCGTTTCGGCGAAACAGGTCCACCATCACGCGTTTGGCGATAGTGCAGAGGAAGGAGCGAGGATCGCGGATCGTCGAGAGCGTTTCGCTGACCATTACCCGCa                           >  1:184064/1‑138 (MQ=255)                                                                     cgcCAGCATCTCCAGATACGCTTTTCCCAGCGCGTTTCGGCGAAACAGGTCCACCATCACGCGTTTGGCGa                                                                                          >  1:72223/1‑71 (MQ=255)                                                                     cgcCAGCATCTCCAGATACGCTTTTCCCAGCGCGTTTCGGCGAAACAGGTCCACCATCACGCGTTTGGCGa                                                                                          <  2:72223/71‑1 (MQ=255)                                                                     cgcCAGCATCTCCAGATACGCTTTTCCCAGCGCGTTTCGGCGAAACAGGTCCACCATCACGCGTTTGGCGATAGTGCAGAGGAAGGAGCGAGGATCGCGGATCGTCGAGAGCGTTTCGCTGACCATTACCCGCaaaaaa                      <  1:150400/139‑1 (MQ=255)                                                                          gCATCTCCAGATACGCTTTTCCCAGCGCGTTTCGGCGAAACAGGTCCACCATCACGCGTTTGGCGATAGTGCAGAGGAAGGAGCGAGGATCGCGGATCGTCGAGAGCGTTTCGCTGACCATTACCCGCAAAAAAGTGTc                 <  2:184064/139‑1 (MQ=255)                                                                                   gATACGCTTTTCCCAGCGCGTTTCGGCGAAACAGGTCCACCATCACGCGTTTGGCGATAGTGCAGAGGAAGGAGCGAGGATCGCGGATCGTCGAGAGCGTTTCGCTGACCATTACCCGCAAAAAAGTGTCCTGGGCAAt        <  2:370647/139‑1 (MQ=255)                                                                                         cTTTTCCCAGCGCGTTTCGGCGAAACAGGTCCACCATCACGCGTTTGGCGATAGTGCAGAGGAAGGAGCGAGGATCGCGGATCGTCGAGAGCGTTTCGCTGACCATTACCCGCAAAAAAGTGTCCTGGGCAATGTCATc  >  2:104164/1‑139 (MQ=255)                                                                                         cTTTTCCCAGCGCGTTTCGGCGAAACAGGTCCACCATCACGCGTTTGGCGATAGTGCAGAGGAAGGAGCGAGGATCGCGGATCGTCGAGAGCGTTTCGCTGACCATTACCCGCAAAAAAGTGTCCTGGGCAATGTCATc  <  2:40595/139‑1 (MQ=255)                                                                                         cTTTTCCCAGCGCGTTTCGGCGAAACAGGTCCACCATCACGCGTTTGGCGATAGTGCAGAGGAAGGAGCGAGGATCGCGGATCGTCGAGAGCGTTTCGCTGACCATTACCCGCAAAAAAGTGTCCTGGGCAATGTCATc  >  1:201144/1‑139 (MQ=255)                                                                                              |                                                                                                                                      AGGAGTTGTAGGGTCTCGAGTTGGCTTTCGCGTTCCTCAGGTGAAGGCGCTCCCCCCTCCGGCATAAGCGCCAGCATCTCCAGATACGCTTTTTCCAGCGCGTTTCGGCGAAACAGGTCCACCATCACGCGTTTGGCGATAGTGCAGAGGAAGGAGCGAGGATCGCGGATCGTCGAGAGCGTTTCGCTGACCATTACCCGCAAAAAAGTGTCCTGGGCAATGTCATC  >  NZ_CP009273/4507712‑4507938

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑