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%	152.4 / NA	41	E83G (GAA→GGA)	fecI	RNA polymerase sigma factor FecI
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (18/23);  total (18/23)

GTTTAGCCCGTCCAGCATGCTGTCGAGGAGTTGTAGGGTCTCGAGTTGGCTTTCGCGTTCCTCAGGTGAAGGCGCTCCCCCCTCCGGCATAAGCGCCAGCATCTCCAGATACGCTTTTTCCAGCGCGTTTCGGCGAAACAGGTCCACCATCACGCGTTTGGCGATAGTGCAGAGGAAGGAGCGAGGATCGCGGATCGTCGAGAGCGTTTCGCTGACCATTACCCGCAAAAAAGTGTCCTGGGCAATGTCA  >  NZ_CP009273/4507687‑4507936                                                                                                                       |                                                                                                                                    gTTTAGCCCGTCCAGCATGCTGTCGAGGAGTTGTAGGGTCTCGAGTTGGCTTTCGCGTTCCTCAGGTGAAGGCGCTCCCCCCTCCGGCATAAGCGCCAGCATCTCCAGATACGCTTTTCCCAGCGCGTTTCGGCGAAAc                                                                                                                 <  1:219545/139‑1 (MQ=255)           tCCAGCATGCTGTCGAGGAGTTGTAGGGTCTCGAGTTGGCTTTCGCGTTCCTCAGGTGAAGGCGCTCCCCCCTCCGGCATAAGCGCCAGCATCTCCAGATACGCTTTTCCCAGCGCGTTTCGGCGAAACAGGTccacca                                                                                                       >  2:495341/1‑139 (MQ=255)                     tGTCGAGGAGTTGTAGGGTCTCGAGTTGGCTTTCGCGTTCCTCAGGTGAAGGCGCTCCCCCCTCCGGCATAAGCGCCAGCATCTCCAGATACGCTTTTCCCAGCGCGTTTCGGCGAAACAGGTCCACCATCACGCGttt                                                                                             >  1:116727/1‑139 (MQ=255)                     tGTCGAGGAGTTGTAGGGTCTCGAGTTGGCTTTCGCGTTCCTCAGGTGAAGGCGCTCCCCCCTCCGGCATAAGCGCCAGCATCTCCAGATACGCTTTTCCCAGCGCGTTTCGGCGAAACAGGTCCACCATCACGCGttt                                                                                             >  2:55237/1‑139 (MQ=255)                     tGTCGAGGAGTTGTAGGGTCTCGAGTTGGCTTTCGCGTTCCTCAGGTGAAGGCGCTCCCCCCTCCGGCATAAGCGCCAGCATCTCCAGATACGCTTTTCCCAGCGCGTTTCGGCGAAACAGGTCCACCATCACGCGttt                                                                                             >  1:479191/1‑139 (MQ=255)                       tCGAGGAGTTGTAGGGTCTCGAGTTGGCTTTCGCGTTCCTCAGGTGAAGGCGCTCCCCCCTCCGGCATAAGCGCCAGCATCTCCAGATACGCTTTTCCCAGCGCGTTTCGGCGAAACAGGTCCACCATCACGCGttt                                                                                             <  2:213838/137‑1 (MQ=255)                          aggagTTGTAGGGTCTCGAGTTGGCTTTCGCGTTCCTCAGGTGAAGGCGCTCCCCCCTCCGGCATAAGCGCCAGCATCTCCAGATACGCTTTTCCCAGCGCGTTTCGGCGAAACAGGTCCACCATCACGCGTTTGGCGa                                                                                        <  1:7681/139‑1 (MQ=255)                          aggagTTGTAGGGTCTCGAGTTGGCTTTCGCGTTCCTCAGGTGAAGGCGCTCCCCCCTCCGGCATAAGCGCCAGCATCTCCAGATACGCTTTTCCCAGCGCGTTTCGGCGAAACAGGTCCACCATCACGCGTTTGGCGa                                                                                        <  1:495341/139‑1 (MQ=255)                          aggagTTGTAGGGTCTCGAGTTGGCTTTCGCGTTCCTCAGGTGAAGGCGCTCCCCCCTCCGGCATAAGCGCCAGCATCTCCAGATACGCTTTTCCCAGCGCGTTTCGGCGAAACAGGTCCACCATCACGCGTTTGGCGa                                                                                        <  1:471794/139‑1 (MQ=255)                                      gTCTCGAGTTGGCTTTCGCGTTCCTCAGGTGAAGGCGCTCCCCCCTCCGGCATAAGCGCCAGCATCTCCAGATACGCTTTTCCCAGCGCGTTTCGGCGAAACAGGTCCACCATCACGCGTTTGGCGATAGTGCAGagga                                                                            <  2:14229/139‑1 (MQ=255)                                       tctcGAGTTGGCTTTCGCGTTCCTCAGGTGAAGGCGCTCCCCCCTCCGGCATAAGCGCCAGCATCTCCAGATACGCTTTTCCCAGCGCGTTTCGGCGAAACAGGTCCACCATCACGCGTTTGGCGATAGTGCAGaggaa                                                                           <  2:116727/139‑1 (MQ=255)                                        ctcGAGTTGGCTTTCGCGTTCCTCAGGTGAAGGCGCTCCCCCCTCCGGCATAAGCGCCAGCATCTCCAGATACGCTTTTCCCAGCGCGTTTCgg                                                                                                                       <  2:233803/94‑1 (MQ=255)                                        ctcGAGTTGGCTTTCGCGTTCCTCAGGTGAAGGCGCTCCCCCCTCCGGCATAAGCGCCAGCATCTCCAGATACGCTTTTCCCAGCGCGTTTCgg                                                                                                                       >  1:233803/1‑94 (MQ=255)                                         tcGAGTTGGCTTTCGCGTTCCTCAGGTGAAGGCGCTCCCCCCTCCGGCATAAGCGCCAGCATCTCCAGATACGCTTTTCCCAGCGCGTTTCGGCGAAAc                                                                                                                 >  2:324778/1‑99 (MQ=255)                                         tcGAGTTGGCTTTCGCGTTCCTCAGGTGAAGGCGCTCCCCCCTCCGGCATAAGCGCCAGCATCTCCAGATACGCTTTTCCCAGCGCGTTTCGGCGAAAc                                                                                                                 <  1:324778/99‑1 (MQ=255)                                         tcGAGTTGGCTTTCGCGTTCCTCAGGTGAAGGCGCTCCCCCCTCCGGCATAAGCGCCAGCATCTCCAGATACGCTTTTCCCAGCGCGTTTCGGCGAAACAGGTCCACCATCACGCGttt                                                                                             <  1:371346/119‑1 (MQ=255)                                         tcGAGTTGGCTTTCGCGTTCCTCAGGTGAAGGCGCTCCCCCCTCCGGCATAAGCGCCAGCATCTCCAGATACGCTTTTCCCAGCGCGTTTCGGCGAAACAGGTCCACCATCACGCGttt                                                                                             >  2:371346/1‑119 (MQ=255)                                         tcGAGTTGGCTTTCGCGTTCCTCAGGTGAAGGCGCTCCCCCCTCCGGCATAAGCGCCAGCATCTCCAGATACGCTTTTCCCAGCGCGTTTCGGCGAAACAGGTCCACCATCACGCGTTTGGCGATAGTGCAGaggaag                                                                          >  2:332694/1‑138 (MQ=255)                                         tcGAGTTGGCTTTCGCGTTCCTCAGGTGAAGGCGCTCCCCCCTCCGGCATAAGCGCCAGCATCTCCAGATACGCTTTTCCCAGCGCGTTTCGGCGAAACAGGTCCACCATCACGCGTTTGGCGATAGTGCAGaggaag                                                                          >  2:151189/1‑138 (MQ=255)                                                 gCTTTCGCGTTCCTCAGGTGAAGGCGCTCCCCCCTCCGGCATAAGCGCCAGCATCTCCAGATACGCTTTTCCCAGCGCGTTTCGGCGAAACAGGTCCACCATCACGCGTTTGGCGATAGTGCAGAGGAAGGAGCGAGGa                                                                 <  1:345407/139‑1 (MQ=255)                                                 gCTTTCGCGTTCCTCAGGTGAAGGCGCTCCCCCCTCCGGCATAAGCGCCAGCATCTCCAGATACGCTTTTCCCAGCGCGTTTCGGCGAAACAGGTCCACCATCACGCGTTTGGCGATAGTGCAGAGGAAGGAGCGAGGa                                                                 <  1:327521/139‑1 (MQ=255)                                                  cTTTCGCGTTCCTCAGGTGAAGGCGCTCCCCCCTCCGGCATAAGCGCCAGCATCTCCAGATACGCTTTTCCCAGCGCGTTTCGGCGAAACAGGTCCACCATCACGCGTTTGGCGATAGTGCAGAGGAAGGAGCGAGGAt                                                                <  2:566773/139‑1 (MQ=255)                                                       gcgTTCCTCAGGTGAAGGCGCTCCCCCCTCCGGCATAAGCGCCAGCATCTCCAGATACGCTTTTCCCAGCGCGTTTCGGCGAAACAGGTCCACCATCACGCGTTTGGCGATAGTGCAGAGGAAGGAGCGAGGATCGCgg                                                           <  2:479191/139‑1 (MQ=255)                                                        cgTTCCTCAGGTGAAGGCGCTCCCCCCTCCGGCATAAGCGCCAGCATCTCCAGATACGCTTTTCCCAGCGCGTTTCGGCGAAACAGGTCCACCATCACGCGTTTGGCGATAGTGCAGAGGAAGGAGCGAGGATCGCGGa                                                          <  2:381265/139‑1 (MQ=255)                                                                       ggCGCTCCCCCCTCCGGCATAAGCGCCAGCATCTCCAGATACGCTTTTCCCAGCGCGTTTCGGCGAAACAGGTCCACCATCAcg                                                                                                  >  2:234008/1‑84 (MQ=255)                                                                       ggCGCTCCCCCCTCCGGCATAAGCGCCAGCATCTCCAGATACGCTTTTCCCAGCGCGTTTCGGCGAAACAGGTCCACCATCAcg                                                                                                  <  1:234008/84‑1 (MQ=255)                                                                           cTCCCCCCTCCGGCATAAGCGCCAGCATCTCCAGATACGCTTTTCCCAGTGCGTTTCGGCGAAACAGGTCCACCATCACGCGTTTGGCGATAGTGCAGAGGAAGGAGCGAGGATCGCGGATCGTCGAGAGCGTTTCGCt                                       <  1:344685/139‑1 (MQ=255)                                                                            tCCCCCCTCCGGCATAAGCGCCAGCATCTCCAGATACGCTTTTCCCAGCGCGTTTCGGCGAAACAGGTCCACCATCACGCGTTTGGCGATAGTGCAGAGGAAGGAGCGAGGATCGCGGATCGTCGAGAGCGTTTCGCt                                       >  1:130946/1‑138 (MQ=255)                                                                            tCCCCCCTCCGGCATAAGCGCCAGCATCTCCAGATACGCTTTTCCCAGCGCGTTTCGGCGAAACAGGTCCACCATCACGCGTTTGGCGATAGTGCAGAGGAAGGAGCGAGGATCGCGGATCGTCGAGAGCGTTTCGCt                                       >  1:61054/1‑138 (MQ=255)                                                                                        cATAAGCGCCAGCATCTCCAGATACGCTTTTCCCAGCGCGTTTCGGCGAAACAg                                                                                                               <  2:223610/54‑1 (MQ=255)                                                                                        cATAAGCGCCAGCATCTCCAGATACGCTTTTCCCAGCGCGTTTCGGCGAAACAg                                                                                                               >  1:223610/1‑54 (MQ=255)                                                                                              cgcCAGCATCTCCAGATACGCTTTTCCCAGCGCGTTTCGGCGAAACAGGTCCACCATCACGCGTTTGGCGATAGTGCAGAGGAAGGAGCGAGGATCGCGGATCGTCGAGAGCGTTTCGCTGACCATTACCCGCaaaaaa                    <  2:324441/139‑1 (MQ=255)                                                                                              cgcCAGCATCTCCAGATACGCTTTTCCCAGCGCGTTTCGGCGAAACAGGTCCACCATCACGCGTTTGGCGATAGTGCAGAGGAAGGAGCGAGGATCGCGGATCGTCGAGAGCGTTTCGCTGACCATTACCCGCaaaaaa                    <  2:130946/139‑1 (MQ=255)                                                                                                 cAGCATCTCCAGATACGCTTTTCCCAGCGCGTTTCGGCGAAACAGGTCCACCATCACGCGTTTGGCGATAGTGCAGAGGAAGGAGCGAGGATCGCGGATCGTCGAGAGCGTTTCGCTGACCATTACCCGCAAAAAAgtg                 >  1:170527/1‑139 (MQ=255)                                                                                                  aGCATCTCCAGATACGCTTTTCCCAGCGCGTTTCGGCGAAACAGGTCCACCATCACGCGTTTGGCGATAGTGCAGAGGAAGGAGCGAGGATCGCGGATCGTCGAGAGCGTTTCGCTGACCATTACCCGCAAAAAAgtgt                >  1:263361/1‑139 (MQ=255)                                                                                                  aGCATCTCCAGATACGCTTTTCCCAGCGCGTTTCGGCGAAACAGGTCCACCATCACGCGTTTGGCGATAGTGCAGAGGAAGGAGCGAGGATCGCGGATCGTCGAGAGCGTTTCGCTGACCATTACCCGCAAAAAAgtgt                >  2:120231/1‑139 (MQ=255)                                                                                                   gCATCTCCAGATACGCTTTTCCCAGCGCGTTTCGGCGAAACAGGTCCACCATCACGCGTTTGGCGATAGTGCAGAGGAAGGAGCGAGGATCGCGGATCGTCGAGAGCGTTTCGCTGACCATTACCCGCAAAAAAGTGTc               <  2:526463/139‑1 (MQ=255)                                                                                                          cAGATACGCTTTTCCCAGCGCGTTTCGGCGAAACAGGTCCACCATCACGCGTTTGGCGATAGTGCAGAGGAAGGAGCGAGGATCGCGGATCGTCGAGAGCGTTTCGCTGACCATTACCCGCAAAAAAGTGTCCTGGGCa        <  1:506734/139‑1 (MQ=255)                                                                                                                cGCTTTTCCCAGCGCGTTTCGGCGAAACAGGTCCACCATCACGCGTTTGGCGATAGTGCAGAGGAAGGAGCGAGGATCGCGGATCGTCGAGAGCGTTTCGCTGACCATTACCCGCAAAAAAGTGTCCTGGGCAATGTCa  >  2:427032/1‑139 (MQ=255)                                                                                                                  cTTTTCCCAGCGCGTTTCGGCGAAACAGGTCCACCATCACGCGTTTGGCGATAGTGCAGAGGAAGGAGCGAGGATCGCGGATCGTCGAGAGCGtt                                            >  2:478221/1‑95 (MQ=255)                                                                                                                  cTTTTCCCAGCGCGTTTCGGCGAAACAGGTCCACCATCACGCGTTTGGCGATAGTGCAGAGGAAGGAGCGAGGATCGCGGATCGTCGAGAGCGtt                                            <  1:478221/95‑1 (MQ=255)                                                                                                                       |                                                                                                                                    GTTTAGCCCGTCCAGCATGCTGTCGAGGAGTTGTAGGGTCTCGAGTTGGCTTTCGCGTTCCTCAGGTGAAGGCGCTCCCCCCTCCGGCATAAGCGCCAGCATCTCCAGATACGCTTTTTCCAGCGCGTTTCGGCGAAACAGGTCCACCATCACGCGTTTGGCGATAGTGCAGAGGAAGGAGCGAGGATCGCGGATCGTCGAGAGCGTTTCGCTGACCATTACCCGCAAAAAAGTGTCCTGGGCAATGTCA  >  NZ_CP009273/4507687‑4507936

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑